From csb_tom_new at sina.com Fri Oct 1 05:47:47 2010
From: csb_tom_new at sina.com (csb_tom_new at sina.com)
Date: Fri, 01 Oct 2010 20:47:47 +0800
Subject: [protege-discussion] How to run and debug swrl-jess-bridge?
Message-ID: <20101001124747.226EFFB3402@mail3-19.sinamail.sina.com.cn>
Hello, Martin!
I think that I'm not adept in Java. Comparatively, I'm a little more familiar with C++. Now I have to study Java according to C++ experience. The IDE I use is Eclipse 3.5(Galileo). I download sourcecode of protege-core, protege-owl, swrl-jess-bridge (with version of 3.4.4) from sourcecode subversion server of Protege. I have smoothly compile these 3 sourcecodes. The configuration is protege-owl depends on protege-core, and swrl-jess-bridge depends on protege-core and protege-owl.
I found that Protege-core and protege-owl have file containing main() function. In Protege-core the file is Application.java and in protege-owl the file is ProtegeOWL.java, but in swrl-jess-bridge, there is no file which contains main() function. Therefore, I can debug and trace protege-core or protege-owl, but I can not debug and trace swrl-jess-bridge. I think here need some special configuration. Can you tell me how to do this?
Thank you very much!
Tom
>Protege-OWL and all the SWRLTab components (including the Jess back end)
>are pretty standard Java software. The IDE that you are using will
>govern how you will run and debug the software.
>
>What IDE are you using?
From tredmond at stanford.edu Fri Oct 1 11:51:52 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Fri, 01 Oct 2010 11:51:52 -0700
Subject: [protege-discussion] Inferencing Problem
In-Reply-To: <530975.13342.qm@web39603.mail.mud.yahoo.com>
References: <530975.13342.qm@web39603.mail.mud.yahoo.com>
Message-ID: <4CA62DC8.1080806@stanford.edu>
> what i should do? is there something wrong with protege 4.1 beta
> source ? does i need to download the source again?
I am doubting that there is any problem with your copy of Protege.
Build 209 is recommended (Help->About).
You need to do the following steps:
1. Open the attached ontology in Protege 4.1.
2. To see inferences you need a reasoner. In the Reasoner menu,
select the HermiT reasoner. Then select classify.
3. You will also need to turn on the display of these inferences in
the reasoner configuration. Go to Reasoner->Configure, select
the displayed inferences, and make sure that the three items in
the "Displayed Individual Inferences" are selected.
4. Go to the Individuals tab, select the class A and then select the
individual i and you should see the desired inferences.
-Timothy
On 09/30/2010 11:48 AM, Soha Said wrote:
> Hello,
> What is the problem with my application?
> why i didn't get the same results like your sample ontology capture
> you sent.
> I tried to use your owl file and open it in my protege
> and i got wrong inference again.
> what i should do? is there something wrong with protege 4.1 beta
> source ? does i need to download the source again?
> --------------------------------------------------------------
> first question: yes, it captures, but mine doesn't
> my ontology.
> second question: i want to see like the attached image to see the
> different
> parameters in same individual after reasoning.
>
> and I adjust before configuration in reasoning to display datatype
> assertions to
> individuals.
> ---------------------------------------------------------
>
> Two questions.? Does the attached ontology capture what you are trying
> to say?? In what way are you not seeing the desired inference (see the
> attached image)?
>
> -Timothy
>
>
> On 09/21/2010 08:22 AM, Soha Said wrote:
> >
> > Hello,
> >
> > Now,
> >
> > Individual y with data property name="chris".
> >
> > And individual x with data property age=13.
> >
> > And Individual y is same as x.
> >
> > When I query on dl query tab get the following:
> >
> > Individuals that have name value "chris" and age value 13.
> >
> > I got result:
> >
> > Individual x,
> >
> > Individual y.
> >
> > That is good
> >
> > But what I need in my application, that is when x is same as y
> >
> > When I open each individual of them, to see all data properties, such
> > that:
> >
> > Individual x:
> >
> > Name="chris"
> >
> > Age=13
> >
> > Individual y:
> >
> > Name="chris"
> >
> > Age=13
> >
> > But what happen that, when I open each individual I see:
> >
> > Individual x:
> >
> > Name="chris"
> >
> > Individual y:
> >
> > Age=13
> >
> > But when I query ontology, I got write results, as I have shown above.
> >
> > Finally, I want to see all properties in each individual separately
> > and equal, so that I can delete one and keep the other. And this is a
> > very important issue in my application.
> >
> > Also, I need a guide to help me in how to write a rule in prot?g? 4.1
> > beta.
> >
> > I wish that I explain my problem clear now, if someone can help me.
> >
> > Thanks in advance,
> >
> > Soha Said
> >
> > -------------------------------------------------------
> >
> > I suspect that? the core issue is what you mean by
> >
> > > but what happen not that
> > >
> > > still each individual has his own data properties after inferencing
> > >
> > > and I adjust preferences of reasoner. I don't know why?
> > >
> >
> > The attached ontology seems to be what? you are describing.? In that
> > ontology a reasoner will infer that x has data property (age=13) and y
> > has name Chris.? In particular in the latest Protege 4.1 if I
> >
> >? 1. classify the ontology
> >? 2. configure the reasoner (Reasoner->Configure->Displayed Inferences)
> >? ? ? to show "Data Property? Assertions"
> >? 3. go to the Individuals tab and select person and then select x or? y
> >
> >
> > then I will see? the inferences that you are talking about.
> >
> > -Timothy
> >
> >
> > On 09/19/2010 07:17 AM, Soha Said wrote:
> > >
> > > Thanks so much. you got so closed
> > >
> > > I do what you said.
> > >
> > > now individual? x has data property (name="Chris")
> > >
> > > and individual y has data property (age=13)
> > >
> > > after they are same the output must be
> > >
> > > individual x: name="Chris" and age="13"
> > >
> > > and individual y: name="Chris" and age="13"
> > >
> > > but what happen not that
> > >
> > > still each individual has his own data properties after inferencing
> > >
> > > and I adjust preferences of reasoner. I don't know why?
> > >
> > > --------------------------------------------------------
> > >
> > > From: Timothy Redmond
> > >
> > >
> >>>
> > >
> > > Maybe? you are asking whether two individuals that are the same as
> each
> > > other should have the same inferred object and data property values?
> > > The answer is yes.? What's more - this I wasn't clear on - this is
> > > displayed naturally in the latest Protege.? (I knew? from previous
> > > discussions that data property values can be difficult for a reasoner
> > > to compute but I didn't entirely understand why this was so.)
> > >
> > > I created the attached ontology.? In the latest Protege 4.1, I
> selected
> > > my reasoner (I tried both pellet and HermiT).? I changed the reasoner
> > > preferences (Reasoner->Configure->Displayed Inferences) to display
> both
> > > object property assertions and data property assertions.? Then in the
> > > individuals tab I selected? the class A and the individual? j.? It
> then
> > > showed both the inferred data property and inferred object
> property that
> > > was retrieved from? the same individual i.
> > >
> > > -Timothy
> > >
> > >
> > > On 09/17/2010 10:25 AM, Timothy Redmond wrote:
> > > > On 09/17/2010 10:05 AM, Soha Said wrote:
> > > >> Hello,
> > > >> I put some rule says that: if person x ,student y , y is copluar to
> > > >> (some relation in my ontology) x, y is nsubj to (some relation
> in my
> > > >> ontology) x then x same as y.
> > > >> this rule when applied data properties and object properties
> must be
> > > >> equaled? of x and y.but what happened object properties are equaled
> > > >> but data properties are not equaled. why?
> > > >
> > > > Again I have trouble understanding your question.? The rule you
> > > > describe? is as follows:
> > > >
> > > >? ? Person(x)
> > > >? ? Student(y)
> > > >? ? y copluar x
> > > >? ? x nsubj y
> > > >? ? ---------------
> > > >? ? x = y
> > > >
> > > >
> > > >
> > > > I am not sure if there are any SWRL constraints? about the
> conclusion
> > > > (x=y) but I will ignore that for the moment.? There are not data
> > > > properties in this rule.? In this rule, x and y must be
> individuals so
> > > > the properties, copluar and nsubj,? must be object properties.? I
> > > > would have guessed that the x and y are the only variables in this
> > > > rule so this rule only applies to people and students.? It cannot be
> > > > applied to data properties.
> > > >
> > > > -Timothy
> > > >
> > > >
> > > >> Thanks in advance,
> > > >> Soha Said
> > > >>
> > >
>
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From patricia.charlton at pobox.com Fri Oct 1 13:49:42 2010
From: patricia.charlton at pobox.com (Patricia Charlton)
Date: Fri, 1 Oct 2010 21:49:42 +0100
Subject: [protege-discussion] loading protege files from a resource
Message-ID:
Hi there,
I would like to be able to set the path at run time to load the
protege files (pprj, pont and pins) from JAVA into a JESS engine
e.g.
engine.executeCommand("(load-project LDSEv6June2010.pprj)");
will load PPRJ file from current directory or I can set it to load
from another directory but pont and pins files always want to be found
either in current directory or at the root.
Is there something I need to do so that the path to pont and pins
files to provide the path at run time ? is this possible?
Does anyone know a way around this?
Kind regards,
Patricia
From plwhetzel at gmail.com Fri Oct 1 14:45:09 2010
From: plwhetzel at gmail.com (Trish Whetzel)
Date: Fri, 1 Oct 2010 14:45:09 -0700
Subject: [protege-discussion] NCBO Webinar - Andrew Su and Ben Good,
October 6 at 10:00am PT
In-Reply-To:
References:
Message-ID:
The next NCBO Webinar will be presented by Drs. Andrew Su and Ben Good from
the Genomics Institute of the Novartis Research Foundation on "The Gene
Wiki: Cultivating and mining community intelligence in biology" at 10:00am
PDT, Wednesday, October 6. Below is information on how to join the online
meeting via WebEx and accompanying teleconference. Please note there will
not be a VOIP option and attendees must call into the teleconference. For
the full schedule of the NCBO Webinar presentations see:
http://www.bioontology.org/webinar-series.
ABSTRACT:
The goal of the Gene Wiki is to create a continuously-updated,
collaboratively-written, and community-reviewed review article for every
gene in the human genome. The Gene Wiki currently takes the form of ~10,000
Wikipedia articles, each describing one human gene. In total, the Gene Wiki
contains over 65 MB of text content. It receives over four million page
views and one thousand edits per month. Having attained a sizeable and
growing volume of content, one major area of emphasis is improving the
computability of this resource. Specifically, we will describe our efforts
to mine candidate structured gene annotations from community-contributed
text in the Gene Wiki.
BIO:
Andrew Su has been at the Genomics Institute of the Novartis Research
Foundation (GNF) since 2002 where he is currently the Associate Director of
Bioinformatics. One focus of his research is building tools to harness the
intelligence of communities. The Gene Wiki (
http://en.wikipedia.org/wiki/Portal:Gene_Wiki) and BioGPS (
http://biogps.gnf.org) are the two primary applications in this area.
Andrew received his Ph.D. from the Scripps Research Institute and did his
undergraduate at Northwestern University. To overcome his deep-seated
ignorance of ontologies and their applications, Andrew hired Ben Good as a
personal tutor. More importantly, Ben leads the effort to structure Gene
Wiki content. Ben has been a postdoctoral associate at GNF since May 2010.
Prior to that, he received his Ph.D. at the University of British Columbia,
M.Sc. at the University of Sussex, and BS at UC San Diego.
WEBEX DETAILS:
Topic: NCBO Webinar Series
Date: Wednesday, October 6, 2010
Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00)
Meeting Number: 926 719 478
Meeting Password: ncbomeeting
-------------------------------------------------------
To join the online meeting (Now from the Apple iPhone (R) and other
smartphones!)
-------------------------------------------------------
1. Go to
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NZDUwYTM4MmI3&RT=MiM0
2. If requested, enter your name and email address.
3. If a password is required, enter the meeting password: ncbomeeting
4. Click "Join".
5. Follow the instructions that appear on your screen.
To view in other time zones or languages, please click the link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NZDUwYTM4MmI3&ORT=MiM0
-------------------------------------------------------
To join the audio conference only
-------------------------------------------------------
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:
https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=107799137&tollFree=0
Access code:926 719 478
-------------------------------------------------------
For assistance
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/mc
2. On the left navigation bar, click "Support".
You can contact me at:
whetzel at stanford.edu
To update this meeting to your calendar program (for example Microsoft
Outlook), click this link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&ICS=UMI&LD=1&RD=2&ST=1&SHA2=sscJxPSrxubkyAnBruXELuZe4XBKeHnhQa70aJiFfUI=&RT=MiM0
WebEx will automatically setup Meeting Manager for Windows the first time
you join a meeting. To save time, you can setup prior to the meeting by
clicking this link:
https://stanford.webex.com/stanford/meetingcenter/mcsetup.php
http://www.webex.com
CCP:+16504293300x926719478#
IMPORTANT NOTICE: This WebEx service includes a feature that allows audio
and any documents and other materials exchanged or viewed during the session
to be recorded. By joining this session, you automatically consent to such
recordings. If you do not consent to the recording, discuss your concerns
with the meeting host prior to the start of the recording or do not join the
session. Please note that any such recordings may be subject to discovery in
the event of litigation.
------------------------------
https://mailman.stanford.edu/mailman/listinfo/ncbo-publictalks
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From sohaelshafey at yahoo.com Sun Oct 3 10:11:39 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Sun, 3 Oct 2010 10:11:39 -0700 (PDT)
Subject: [protege-discussion] Inferencing Problem
Message-ID: <215050.75575.qm@web39605.mail.mud.yahoo.com>
Thanks very much
I check help in protege and i found i installed protege 4.1 build 203 not 209
i download the right version and it worked correct.
Thanks very much
--------------------------
> what i should do? is there something wrong with protege 4.1 beta
> source ? does i need to download the source again?
I am doubting? that there is any problem with your copy of Protege.?
Build 209 is recommended (Help->About).
You need to do the following steps:
? 1. Open? the attached ontology in Protege 4.1.
? 2. To see inferences? you need a reasoner.? In the Reasoner menu,
? ? ? select the HermiT reasoner.? Then select classify.
? 3. You will also need to turn on the display of these? inferences in
? ? ? the? reasoner? configuration.? Go to Reasoner->Configure, select
? ? ? the displayed inferences, and make sure that the three items in
? ? ? the "Displayed Individual Inferences" are selected.
? 4. Go to the Individuals tab, select the class A and then select the
? ? ? individual i and you should see the desired inferences.
-Timothy
On 09/30/2010 11:48 AM, Soha Said wrote:
> Hello,
> What is the problem with my application?
> why i didn't get the same results like your sample ontology capture
> you sent.
> I tried to use your owl file and open it in my protege
> and i got wrong inference again.
> what i should do? is there something wrong with protege 4.1 beta
> source ? does i need to download the source again?
> --------------------------------------------------------------
> first question: yes, it captures, but mine doesn't
> my ontology.
> second question: i want to see like the attached image to see the
> different
> parameters in same individual after reasoning.
>
> and I adjust before configuration in reasoning to display datatype
> assertions to
> individuals.
> ---------------------------------------------------------
>
> Two questions.? Does the attached ontology capture what you are trying
> to say?? In what way are you not seeing the desired inference (see the
> attached image)?
>
> -Timothy
>
>
> On 09/21/2010 08:22 AM, Soha Said wrote:
> >
> > Hello,
> >
> > Now,
> >
> > Individual y with data property name="chris".
> >
> > And individual x with data property age=13.
> >
> > And Individual y is same as x.
> >
> > When I query on dl query tab get the following:
> >
> > Individuals that have name value "chris" and age value 13.
> >
> > I got result:
> >
> > Individual x,
> >
> > Individual y.
> >
> > That is good
> >
> > But what I need in my application, that is when x is same as y
> >
> > When I open each individual of them, to see all data properties, such
> > that:
> >
> > Individual x:
> >
> > Name="chris"
> >
> > Age=13
> >
> > Individual y:
> >
> > Name="chris"
> >
> > Age=13
> >
> > But what happen that, when I open each individual I see:
> >
> > Individual x:
> >
> > Name="chris"
> >
> > Individual y:
> >
> > Age=13
> >
> > But when I query ontology, I got write results, as I have shown above.
> >
> > Finally, I want to see all properties in each individual separately
> > and equal, so that I can delete one and keep the other. And this is a
> > very important issue in my application.
> >
> > Also, I need a guide to help me in how to write a rule in prot?g? 4.1
> > beta.
> >
> > I wish that I explain my problem clear now, if someone can help me.
> >
> > Thanks in advance,
> >
> > Soha Said
> >
> > -------------------------------------------------------
> >
> > I suspect that? the core issue is what you mean by
> >
> > > but what happen not that
> > >
> > > still each individual has his own data properties after inferencing
> > >
> > > and I adjust preferences of reasoner. I don't know why?
> > >
> >
> > The attached ontology seems to be what? you are describing.? In that
> > ontology a reasoner will infer that x has data property (age=13) and y
> > has name Chris.? In particular in the latest Protege 4.1 if I
> >
> >? 1. classify the ontology
> >? 2. configure the reasoner (Reasoner->Configure->Displayed Inferences)
> >? ? ? to show "Data Property? Assertions"
> >? 3. go to the Individuals tab and select person and then select x or? y
> >
> >
> > then I will see? the inferences that you are talking about.
> >
> > -Timothy
> >
> >
> > On 09/19/2010 07:17 AM, Soha Said wrote:
> > >
> > > Thanks so much. you got so closed
> > >
> > > I do what you said.
> > >
> > > now individual? x has data property (name="Chris")
> > >
> > > and individual y has data property (age=13)
> > >
> > > after they are same the output must be
> > >
> > > individual x: name="Chris" and age="13"
> > >
> > > and individual y: name="Chris" and age="13"
> > >
> > > but what happen not that
> > >
> > > still each individual has his own data properties after inferencing
> > >
> > > and I adjust preferences of reasoner. I don't know why?
> > >
> > > --------------------------------------------------------
> > >
> > > From: Timothy Redmond
> > >
> > >
> >>>
> > >
> > > Maybe? you are asking whether two individuals that are the same as
> each
> > > other should have the same inferred object and data property values?
> > > The answer is yes.? What's more - this I wasn't clear on - this is
> > > displayed naturally in the latest Protege.? (I knew? from previous
> > > discussions that data property values can be difficult for a reasoner
> > > to compute but I didn't entirely understand why this was so.)
> > >
> > > I created the attached ontology.? In the latest Protege 4.1, I
> selected
> > > my reasoner (I tried both pellet and HermiT).? I changed the reasoner
> > > preferences (Reasoner->Configure->Displayed Inferences) to display
> both
> > > object property assertions and data property assertions.? Then in the
> > > individuals tab I selected? the class A and the individual? j.? It
> then
> > > showed both the inferred data property and inferred object
> property that
> > > was retrieved from? the same individual i.
> > >
> > > -Timothy
> > >
> > >
> > > On 09/17/2010 10:25 AM, Timothy Redmond wrote:
> > > > On 09/17/2010 10:05 AM, Soha Said wrote:
> > > >> Hello,
> > > >> I put some rule says that: if person x ,student y , y is copluar to
> > > >> (some relation in my ontology) x, y is nsubj to (some relation
> in my
> > > >> ontology) x then x same as y.
> > > >> this rule when applied data properties and object properties
> must be
> > > >> equaled? of x and y.but what happened object properties are equaled
> > > >> but data properties are not equaled. why?
> > > >
> > > > Again I have trouble understanding your question.? The rule you
> > > > describe? is as follows:
> > > >
> > > >? ? Person(x)
> > > >? ? Student(y)
> > > >? ? y copluar x
> > > >? ? x nsubj y
> > > >? ? ---------------
> > > >? ? x = y
> > > >
> > > >
> > > >
> > > > I am not sure if there are any SWRL constraints? about the
> conclusion
> > > > (x=y) but I will ignore that for the moment.? There are not data
> > > > properties in this rule.? In this rule, x and y must be
> individuals so
> > > > the properties, copluar and nsubj,? must be object properties.? I
> > > > would have guessed that the x and y are the only variables in this
> > > > rule so this rule only applies to people and students.? It cannot be
> > > > applied to data properties.
> > > >
> > > > -Timothy
> > > >
> > > >
> > > >> Thanks in advance,
> > > >> Soha Said
> > > >>
> > >
>
>
>
>
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From elena.nardini at unibo.it Mon Oct 4 01:39:46 2010
From: elena.nardini at unibo.it (Elena Nardini)
Date: Mon, 4 Oct 2010 10:39:46 +0200
Subject: [protege-discussion] SPARQL query
Message-ID: <9A46B227-3F42-4C4E-8E6E-8FE5C4336507@unibo.it>
Hi,
is it possible to use SPARQL query in Protege 4.0.2?
Thanks,
Elena
---
Ing. Elena Nardini
Phd Student
DEIS, Alma Mater Studiorum - Universit? di Bologna
Via Venezia, 52
47521 Cesena (FC) - Italy
-------------------------------------------------------
tel: +39 0547 3 39210
fax: +39 0547 3 39208
email: elena.nardini at unibo.it
homepage: http://www.alice.unibo.it/xwiki/bin/view/ElenaNardini/
From hannowun at googlemail.com Tue Oct 5 03:14:43 2010
From: hannowun at googlemail.com (Hanno Wunderlich)
Date: Tue, 5 Oct 2010 12:14:43 +0200
Subject: [protege-discussion] Randomly no displayslots in Protege
Client-Server-Mode until server restart.
Message-ID:
Hi,
we are using Protege Frames (3.4) in Client-Server-Mode with following
project setup:
Project A : Contains only Classes and Slots and formular informations
(including displayslots)
Project B: Includes project A, contains some instances
Project C: Includes project A, contains some instances, contains own
formular informations (including displayslots)
Project D: Includes project C, contains some instance, contains own formular
informations for two classes
Project B,C,D are hosted on our Protege server. All projects were stored in
clips files.
Durinig usage of theese projects we are randomly observing that clients
connecting to a project can load and view it, but the defined display slots
are missing (the default display slot ...Instance_XXXXXXX is used). After
observing this problem and reconnecting to the same project (even from
another client) the display slots are still wrong. The only thing, that
solves the problem is restarting the server.
The interesting thing is, that if the display slots for project C were wrong
that does not mean that they are also wrong when connecting to project B or
D.
As multiple users are accessing the different projects at the same time we
can't always restart the server if one project shows the wrong display
slots.
Is there a way to track down, why this is happening? E.g. what
logging.properties should be used.
Or is there a way to reload only one particular project (or its display
slots) on the server, so that all other users can continue their work?
Regards,
Hanno Wunderlich
PS: Only the display slots seem to be affected. The forms are always loaded
as expected.
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From madhukarg8 at aol.com Tue Oct 5 06:45:30 2010
From: madhukarg8 at aol.com (madhukarg8 at aol.com)
Date: Tue, 05 Oct 2010 09:45:30 -0400
Subject: [protege-discussion] (no subject)
Message-ID: <8CD32AAB5D78D6D-1760-139A4@webmail-m017.sysops.aol.com>
http://www.crown-sa.org/44_7.html
From tredmond at stanford.edu Tue Oct 5 07:02:33 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 05 Oct 2010 07:02:33 -0700
Subject: [protege-discussion] SPARQL query
In-Reply-To: <9A46B227-3F42-4C4E-8E6E-8FE5C4336507@unibo.it>
References: <9A46B227-3F42-4C4E-8E6E-8FE5C4336507@unibo.it>
Message-ID: <4CAB2FF9.6030807@stanford.edu>
Not currently. SPARQL is an RDF style construct and Protege 4 would
have to generate the RDF serialization to support it. The pellet group
has developed SPARQL DL which works better with OWL and it would be cool
if they had some Protege plugin supporting this.
BTW - I would recommend you consider Protege 4.1 as it has better
compatibility with OWL 2 and OWL 1.
-Timothy
On 10/04/2010 01:39 AM, Elena Nardini wrote:
> Hi,
> is it possible to use SPARQL query in Protege 4.0.2?
>
>
> Thanks,
> Elena
> ---
> Ing. Elena Nardini
> Phd Student
> DEIS, Alma Mater Studiorum - Universit? di Bologna
> Via Venezia, 52
> 47521 Cesena (FC) - Italy
> -------------------------------------------------------
> tel: +39 0547 3 39210
> fax: +39 0547 3 39208
> email: elena.nardini at unibo.it
> homepage: http://www.alice.unibo.it/xwiki/bin/view/ElenaNardini/
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
From tredmond at stanford.edu Tue Oct 5 08:57:34 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 05 Oct 2010 08:57:34 -0700
Subject: [protege-discussion] Inferencing Problem
In-Reply-To: <215050.75575.qm@web39605.mail.mud.yahoo.com>
References: <215050.75575.qm@web39605.mail.mud.yahoo.com>
Message-ID: <4CAB4AEE.1090005@stanford.edu>
On 10/03/2010 10:11 AM, Soha Said wrote:
> Thanks very much
> I check help in protege and i found i installed protege 4.1 build 203
> not 209
> i download the right version and it worked correct.
It is true that there have been some changes to the user interface
regarding the reasoners. I usually work with the latest so this makes
sense.
-Timothy
> Thanks very much
> --------------------------
> > what i should do? is there something wrong with protege 4.1 beta
> > source ? does i need to download the source again?
>
> I am doubting that there is any problem with your copy of Protege.
> Build 209 is recommended (Help->About).
>
> You need to do the following steps:
>
> 1. Open the attached ontology in Protege 4.1.
> 2. To see inferences you need a reasoner. In the Reasoner menu,
> select the HermiT reasoner. Then select classify.
> 3. You will also need to turn on the display of these inferences in
> the reasoner configuration. Go to Reasoner->Configure, select
> the displayed inferences, and make sure that the three items in
> the "Displayed Individual Inferences" are selected.
> 4. Go to the Individuals tab, select the class A and then select the
> individual i and you should see the desired inferences.
>
> -Timothy
>
>
>
> On 09/30/2010 11:48 AM, Soha Said wrote:
> > Hello,
> > What is the problem with my application?
> > why i didn't get the same results like your sample ontology capture
> > you sent.
> > I tried to use your owl file and open it in my protege
> > and i got wrong inference again.
> > what i should do? is there something wrong with protege 4.1 beta
> > source ? does i need to download the source again?
> > --------------------------------------------------------------
> > first question: yes, it captures, but mine doesn't
> > my ontology.
> > second question: i want to see like the attached image to see the
> > different
> > parameters in same individual after reasoning.
> >
> > and I adjust before configuration in reasoning to display datatype
> > assertions to
> > individuals.
> > ---------------------------------------------------------
> >
> > Two questions.? Does the attached ontology capture what you are trying
> > to say?? In what way are you not seeing the desired inference (see the
> > attached image)?
> >
> > -Timothy
> >
> >
> > On 09/21/2010 08:22 AM, Soha Said wrote:
> > >
> > > Hello,
> > >
> > > Now,
> > >
> > > Individual y with data property name="chris".
> > >
> > > And individual x with data property age=13.
> > >
> > > And Individual y is same as x.
> > >
> > > When I query on dl query tab get the following:
> > >
> > > Individuals that have name value "chris" and age value 13.
> > >
> > > I got result:
> > >
> > > Individual x,
> > >
> > > Individual y.
> > >
> > > That is good
> > >
> > > But what I need in my application, that is when x is same as y
> > >
> > > When I open each individual of them, to see all data properties, such
> > > that:
> > >
> > > Individual x:
> > >
> > > Name="chris"
> > >
> > > Age=13
> > >
> > > Individual y:
> > >
> > > Name="chris"
> > >
> > > Age=13
> > >
> > > But what happen that, when I open each individual I see:
> > >
> > > Individual x:
> > >
> > > Name="chris"
> > >
> > > Individual y:
> > >
> > > Age=13
> > >
> > > But when I query ontology, I got write results, as I have shown above.
> > >
> > > Finally, I want to see all properties in each individual separately
> > > and equal, so that I can delete one and keep the other. And this is a
> > > very important issue in my application.
> > >
> > > Also, I need a guide to help me in how to write a rule in prot?g? 4.1
> > > beta.
> > >
> > > I wish that I explain my problem clear now, if someone can help me.
> > >
> > > Thanks in advance,
> > >
> > > Soha Said
> > >
> > > -------------------------------------------------------
> > >
> > > I suspect that? the core issue is what you mean by
> > >
> > > > but what happen not that
> > > >
> > > > still each individual has his own data properties after inferencing
> > > >
> > > > and I adjust preferences of reasoner. I don't know why?
> > > >
> > >
> > > The attached ontology seems to be what? you are describing.? In that
> > > ontology a reasoner will infer that x has data property (age=13) and y
> > > has name Chris.? In particular in the latest Protege 4.1 if I
> > >
> > >? 1. classify the ontology
> > >? 2. configure the reasoner (Reasoner->Configure->Displayed Inferences)
> > >? ? ? to show "Data Property? Assertions"
> > >? 3. go to the Individuals tab and select person and then select x
> or? y
> > >
> > >
> > > then I will see? the inferences that you are talking about.
> > >
> > > -Timothy
> > >
> > >
> > > On 09/19/2010 07:17 AM, Soha Said wrote:
> > > >
> > > > Thanks so much. you got so closed
> > > >
> > > > I do what you said.
> > > >
> > > > now individual? x has data property (name="Chris")
> > > >
> > > > and individual y has data property (age=13)
> > > >
> > > > after they are same the output must be
> > > >
> > > > individual x: name="Chris" and age="13"
> > > >
> > > > and individual y: name="Chris" and age="13"
> > > >
> > > > but what happen not that
> > > >
> > > > still each individual has his own data properties after inferencing
> > > >
> > > > and I adjust preferences of reasoner. I don't know why?
> > > >
> > > > --------------------------------------------------------
> > > >
> > > > From: Timothy Redmond
> > >
> > >
> >>
> > > >
> >
> >
> >>>>
> > > >
> > > > Maybe? you are asking whether two individuals that are the same as
> > each
> > > > other should have the same inferred object and data property values?
> > > > The answer is yes.? What's more - this I wasn't clear on - this is
> > > > displayed naturally in the latest Protege.? (I knew? from previous
> > > > discussions that data property values can be difficult for a
> reasoner
> > > > to compute but I didn't entirely understand why this was so.)
> > > >
> > > > I created the attached ontology.? In the latest Protege 4.1, I
> > selected
> > > > my reasoner (I tried both pellet and HermiT).? I changed the
> reasoner
> > > > preferences (Reasoner->Configure->Displayed Inferences) to display
> > both
> > > > object property assertions and data property assertions.? Then
> in the
> > > > individuals tab I selected? the class A and the individual? j.? It
> > then
> > > > showed both the inferred data property and inferred object
> > property that
> > > > was retrieved from? the same individual i.
> > > >
> > > > -Timothy
> > > >
> > > >
> > > > On 09/17/2010 10:25 AM, Timothy Redmond wrote:
> > > > > On 09/17/2010 10:05 AM, Soha Said wrote:
> > > > >> Hello,
> > > > >> I put some rule says that: if person x ,student y , y is
> copluar to
> > > > >> (some relation in my ontology) x, y is nsubj to (some relation
> > in my
> > > > >> ontology) x then x same as y.
> > > > >> this rule when applied data properties and object properties
> > must be
> > > > >> equaled? of x and y.but what happened object properties are
> equaled
> > > > >> but data properties are not equaled. why?
> > > > >
> > > > > Again I have trouble understanding your question.? The rule you
> > > > > describe? is as follows:
> > > > >
> > > > >? ? Person(x)
> > > > >? ? Student(y)
> > > > >? ? y copluar x
> > > > >? ? x nsubj y
> > > > >? ? ---------------
> > > > >? ? x = y
> > > > >
> > > > >
> > > > >
> > > > > I am not sure if there are any SWRL constraints? about the
> > conclusion
> > > > > (x=y) but I will ignore that for the moment.? There are not data
> > > > > properties in this rule.? In this rule, x and y must be
> > individuals so
> > > > > the properties, copluar and nsubj,? must be object properties.? I
> > > > > would have guessed that the x and y are the only variables in this
> > > > > rule so this rule only applies to people and students.? It
> cannot be
> > > > > applied to data properties.
> > > > >
> > > > > -Timothy
> > > > >
> > > > >
> > > > >> Thanks in advance,
> > > > >> Soha Said
> > > > >>
> > > >
> >
> >
> >
> >
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From tredmond at stanford.edu Tue Oct 5 09:08:52 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 05 Oct 2010 09:08:52 -0700
Subject: [protege-discussion] loading protege files from a resource
In-Reply-To:
References:
Message-ID: <4CAB4D94.6000605@stanford.edu>
I don't think that this will work in the way that you are hoping.
-Timothy
On 10/01/2010 01:49 PM, Patricia Charlton wrote:
> Hi there,
>
> I would like to be able to set the path at run time to load the
> protege files (pprj, pont and pins) from JAVA into a JESS engine
> e.g.
> engine.executeCommand("(load-project LDSEv6June2010.pprj)");
>
> will load PPRJ file from current directory or I can set it to load
> from another directory but pont and pins files always want to be found
> either in current directory or at the root.
>
> Is there something I need to do so that the path to pont and pins
> files to provide the path at run time ? is this possible?
> Does anyone know a way around this?
>
> Kind regards,
> Patricia
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
From patricia.charlton at pobox.com Tue Oct 5 12:22:32 2010
From: patricia.charlton at pobox.com (Patricia Charlton)
Date: Tue, 5 Oct 2010 20:22:32 +0100
Subject: [protege-discussion] loading protege files from a resource,
Issue 6
In-Reply-To:
References:
Message-ID:
>
Hi there,
Is there any loading path control at runtime over the files? Or is it
just set by wherever you load the pprj file?
Kind regards,
Patricia
> Message: 1
> Date: Tue, 05 Oct 2010 09:08:52 -0700
> From: Timothy Redmond
> To: protege-discussion at lists.stanford.edu
> Subject: Re: [protege-discussion] loading protege files from a
> resource
> Message-ID: <4CAB4D94.6000605 at stanford.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> I don't think that this will work in the way that you are hoping.
>
> -Timothy
>
>
> On 10/01/2010 01:49 PM, Patricia Charlton wrote:
>> Hi there,
>>
>> I would like to be able to set the path at run time to load the
>> protege files (pprj, pont and pins) from JAVA into a JESS engine
>> e.g.
>> engine.executeCommand("(load-project LDSEv6June2010.pprj)");
>>
>> will load PPRJ file from current directory or I can set it to load
>> from another directory but pont and pins files always want to be
>> found
>> either in current directory or at the root.
>>
>> Is there something I need to do so that the path to pont and pins
>> files to provide the path at run time ? is this possible?
>> Does anyone know a way around this?
>>
>> Kind regards,
>> Patricia
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> ------------------------------
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
>
> End of protege-discussion Digest, Vol 51, Issue 6
> *************************************************
From claudia.damato at di.uniba.it Wed Oct 6 01:26:02 2010
From: claudia.damato at di.uniba.it (Claudia d'Amato)
Date: Wed, 06 Oct 2010 10:26:02 +0200
Subject: [protege-discussion] Call for Chapters: "Collaboration and the
Semantic Web: Social Networks, Knowledge Networks and Knowledge Resources"
Message-ID: <4CAC329A.3070501@di.uniba.it>
***** Apologies for multiple postings ******
-----------------------------------------------------------------------------------------------
Collaboration and the Semantic Web: Social Networks, Knowledge Networks and Knowledge Resources
-----------------------------------------------------------------------------------------------
Editors:
Stefan Br?ggemann, OFFIS, Germany
Claudia d'Amato, University of Bari, Italy
Call for Chapters:
Proposals Submission Deadline: November 1, 2010
Full Chapters Due: March 1, 2011
Submission Date: June 15, 2011
Website http://redir.ec/CollSemWeb
Overview
Social media and the semantic web only co-existed in the past, but when these developments became
massively popular, they began to have an influence on collaborative working. Learners and online
workers now have a variety of knowledge resources at hand. Integrated semantic applications, linked
data, social networks, and networked digital solutions can now be used in collaborative learning
environments and present participants with the context-aware information that they need.
Semantic technologies have shown their potential for integrating valuable knowledge bases and
information systems, and they are being applied to the composition of digital learning and working
platforms. These semantic technologies not only have potential for solving the semantic
heterogeneity of knowledge resources, trust, and accountability, but also provide solutions for
contemporary data quality management cycles, which are necessary to ensure the high-quality
integration of shared knowledge resources.
Objectives
The primary goal of the book is to showcase cutting edge research on the intersection of Semantic
Web, Collaborative Work, and Social Media. For example:
How can richly structured Semantic Web data and existing semantic web technologies together build
next-generation systems for collaborative work?
How could knowledge management techniques contribute to the full realization of integrated semantic
applications?
What are the challenges for developers of social systems with integrated semantic web data?
Audience
The book addresses researchers and practitioners in the fields of semantic web, knowledge
management, data integration, and data quality management by summarizing recent research results.
Developer of systems in the area of semantic web, knowledge management, and data integration are
addressed as well and will get an overview on semantic web, knowledge management, and collaboration.
Topics
The topics of interest of the book include, but are not limited to:
Social Media
Collaborative work
Semantic applications
Semantic technologies
Digital solutions
Networked applications
Networked knowledge
Data quality
Knowledge Discovery and Ontologies
Trust and provenance
Semantic heterogeneity: querying and management
Reasoning methods for handling semantic knowledge
Knowledge management
Knowledge discovery and linked data
Discovering hidden knowledge from linked data
Learning ontologies from linked data
Applications
Challenges in practical applications of semantic technologies on
Social systems
Collaborative working environments
Health informatics
Life sciences
Semantic multimedia
Information systems
Data quality
and others
Submission Process
Researchers and practitioners are invited to submit on or before November 1, 2010, a 2-3 page
chapter proposal clearly explaining the mission and concerns of his or her proposed chapter. Authors
of accepted proposals will be notified by December 1, 2010 about the status of their proposals and
sent chapter guidelines. Full chapters are expected to be submitted by March 1, 2011. All submitted
chapters will be reviewed on a double-blind review basis. Contributors may also be requested to
serve as reviewers for this project.
Dates
1st Proposal Submission Deadline: November 1, 2010
Full chapter Submission: March 1, 2011
Notification: May 15, 2011
Revised Chapter Submission: June 15, 2011
Final Acceptance Notifications: June 30, 2011
Submission of Final Chapters: July 15, 2011
Publisher
This book is scheduled to be published by IGI Global in early 2012. For additional information
regarding the publisher, please visit www.igi-global.com
Inquiries and submissions can be forwarded electronically (Word document):
Stefan Br?ggemann, OFFIS, Germany email: brueggemann (at) offis.de
Claudia d'Amato, University of Bari, Italy email: claudia.damato (at) di.uniba.it
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From madhukarg8 at aol.com Wed Oct 6 02:06:07 2010
From: madhukarg8 at aol.com (madhukarg8 at aol.com)
Date: Wed, 06 Oct 2010 05:06:07 -0400
Subject: [protege-discussion] (no subject)
Message-ID: <8CD334CD8C5DF86-644-8FD1@webmail-m098.sysops.aol.com>
http://virginia.it/und7.html
From manjula_mit at yahoo.com Wed Oct 6 03:22:20 2010
From: manjula_mit at yahoo.com (shenoy manjula)
Date: Wed, 6 Oct 2010 03:22:20 -0700 (PDT)
Subject: [protege-discussion] OWL
Message-ID: <264866.25167.qm@web38701.mail.mud.yahoo.com>
Is there an protegeAPI which converts a owl file into graph? which is that can
anybody suggest how to use it?
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From tredmond at stanford.edu Wed Oct 6 10:39:16 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Wed, 06 Oct 2010 10:39:16 -0700
Subject: [protege-discussion] OWL
In-Reply-To: <264866.25167.qm@web38701.mail.mud.yahoo.com>
References: <264866.25167.qm@web38701.mail.mud.yahoo.com>
Message-ID: <4CACB444.8010908@stanford.edu>
Not that I know of.
On 10/06/2010 03:22 AM, shenoy manjula wrote:
> Is there an protegeAPI which converts a owl file into graph? which is
> that can anybody suggest how to use it?
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From tredmond at stanford.edu Wed Oct 6 10:42:51 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Wed, 06 Oct 2010 10:42:51 -0700
Subject: [protege-discussion] loading protege files from a resource,
Issue 6
In-Reply-To:
References:
Message-ID: <4CACB51B.5090002@stanford.edu>
On 10/05/2010 12:22 PM, Patricia Charlton wrote:
>
>>
> Hi there,
>
> Is there any loading path control at runtime over the files? Or is it
> just set by wherever you load the pprj file?
I don't know what this means. But, although I think that the .pprj file
may be in a clips format, I am not sure what meaningful information you
can obtain by loading it into jess. On the other hand, the location of
the pins and pont files are encoded in the .pprj file. For example:
([ProjectKB_0036_00041] of String
(name "instances_file_name")
(string_value "metaproject.pins"))
-Timothy
>
> Kind regards,
> Patricia
>
>
>> Message: 1
>> Date: Tue, 05 Oct 2010 09:08:52 -0700
>> From: Timothy Redmond
>> To: protege-discussion at lists.stanford.edu
>> Subject: Re: [protege-discussion] loading protege files from a
>> resource
>> Message-ID: <4CAB4D94.6000605 at stanford.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> I don't think that this will work in the way that you are hoping.
>>
>> -Timothy
>>
>>
>> On 10/01/2010 01:49 PM, Patricia Charlton wrote:
>>> Hi there,
>>>
>>> I would like to be able to set the path at run time to load the
>>> protege files (pprj, pont and pins) from JAVA into a JESS engine
>>> e.g.
>>> engine.executeCommand("(load-project LDSEv6June2010.pprj)");
>>>
>>> will load PPRJ file from current directory or I can set it to load
>>> from another directory but pont and pins files always want to be found
>>> either in current directory or at the root.
>>>
>>> Is there something I need to do so that the path to pont and pins
>>> files to provide the path at run time ? is this possible?
>>> Does anyone know a way around this?
>>>
>>> Kind regards,
>>> Patricia
>>>
>>>
>>> _______________________________________________
>>> protege-discussion mailing list
>>> protege-discussion at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>> Instructions for unsubscribing:
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>>
>> End of protege-discussion Digest, Vol 51, Issue 6
>> *************************************************
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
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From csongor.nyulas at stanford.edu Thu Oct 7 17:42:40 2010
From: csongor.nyulas at stanford.edu (Csongor Nyulas)
Date: Thu, 07 Oct 2010 17:42:40 -0700
Subject: [protege-discussion] OWL
In-Reply-To: <4CACB444.8010908@stanford.edu>
References: <264866.25167.qm@web38701.mail.mud.yahoo.com>
<4CACB444.8010908@stanford.edu>
Message-ID: <4CAE6900.6030901@stanford.edu>
This is from the Protege-OWL mailing list:
http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/20631
Maybe it can be of help to you.
Csongor
On 10/6/2010 10:39 AM, Timothy Redmond wrote:
>
> Not that I know of.
>
> On 10/06/2010 03:22 AM, shenoy manjula wrote:
>> Is there an protegeAPI which converts a owl file into graph? which is
>> that can anybody suggest how to use it?
>>
>>
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From stellato at info.uniroma2.it Fri Oct 8 10:52:07 2010
From: stellato at info.uniroma2.it (Armando Stellato)
Date: Fri, 8 Oct 2010 19:52:07 +0200
Subject: [protege-discussion] Call for Chapters: "Semi-Automatic Ontology
Development: Processes and Resources"
Message-ID: <025501cb6711$8a802530$9f806f90$@uniroma2.it>
***** Apologies for multiple postings ******
----------------------------------------------------------------
Call for Chapters for a new book by IGI Global:
Semi-Automatic Ontology Development: Processes and Resources
----------------------------------------------------------------
Web site: http://art.uniroma2.it/books/saod
Editors:
Maria Teresa Pazienza and Armando Stellato
ART research group (http://art.uniroma2.it/),
University of Tor Vergata, Rome, Italy.
Call for Chapters:
Proposals Submission Deadline: November 15, 2010
Full Chapters Due: January 15, 2011
Introduction:
Exploitation of theoretical results in knowledge representation, language
standardization by W3C and data publication initiatives such as Linked Open
Data have definitively given concreteness to the field of ontology research.
In light of these outcomes, ontology development has also found its way,
benefiting from years of R&D on ontology development tools.
However, while basic development and management technologies have reached a
wide consensus in both academia and industry, those ?more intelligent?
aspects focused on how to automate these processes, how to reuse existing
resources (from raw textual sources to structured / linguistic resources) to
improve existing knowledge, and how to properly interact with different kind
of users, are failing to reach industry-standards. Despite interesting and
promising results from the area of ontology learning, scientifically proven
both on quality and performance of algorithms and on user perspective, there
is a daily evidence that ?ontologists? are not really exploiting these
results, and support from robust and usable tools is quite far from being
available.
The next quantum leap in ontology research should thus properly address
these high-level aspects: resource reuse (linguistic resources, thesauri
etc..), enrichment of contents, networking, support for collaboration
between different experts (domain experts, ontologists, engineers etc
) and
user-tailored interfaces.
Objective of the Book:
This book will aim to provide relevant theoretical frameworks and the latest
empirical research findings in the ontology development and knowledge
acquisition areas. It will be written for both researchers willing to find
new scientific approaches on knowledge acquisition and management in a
homogeneous framework and professionals who want to improve their
understanding of these aspects.
Target Audience:
This book seeks original contributions (or major revision/extensions to
previous work) containing visionary approaches, mature research results and
descriptions of developed tools/frameworks related to optimizing effort and
time required to build Semantic Web Knowledge Resources (from thesauri to
ontologies) and to improve their quality.
Recommended topics include (but are not limited to):
- Improving the ontology life cycle through use of (semi)automatic tools
- Smart acquisition of information extracted from text
- Development of ontologies through reuse of external information from
thesauri / linguistic resources etc
- Intelligent Visual Interfaces for improving ontology developer / domain
expert experience
- Collaboration and Coordination platforms for ontology development for
letting different experts (domain experts, ontologists, knowledge engineers
etc
) cooperate in the creation/maintenance of knowledge resources
Submission Procedure:
Researchers and practitioners are invited to submit on or before November
15th, 2010, a 2-3 page chapter proposal clearly explaining the mission and
concerns of his or her proposed chapter. Authors of accepted proposals will
be notified by November 27th about the status of their proposals and sent
chapter guidelines. Full chapters are expected to be submitted by January
15th, 2011. All submitted chapters should not exceed 15,000 words and should
be sent as a manuscript formatted with MS Word, according to the template
available at:
http://www.igi-global.com/Files/AuthorEditor/extendedtemplate.doc
All chapters will be reviewed on a double-blind review basis. Contributors
may also be requested to serve as reviewers for this project.
Publisher:
This book is scheduled to be published by IGI Global (formerly Idea Group
Inc.), publisher of the ?Information Science Reference? (formerly Idea Group
Reference), ?Medical Information Science Reference,? ?Business Science
Reference,? and ?Engineering Science Reference? imprints. For additional
information regarding the publisher, please visit www.igi-global.com. This
publication is anticipated to be released in 2011.
Important Dates
November 15, 2010: Proposal Submission Deadline (email to the editors a
brief description of the chapter you plan to submit)
November 27, 2010: Notification of Proposal Acceptance
January 15, 2011: Full Chapter Submission
March 30, 2011: Review Results Returned/Acceptance Notification
April 20, 2011: Revised Chapter Submission
May 10, 2011: Final Acceptance Notification
May 30, 2011: Final Chapter Submission
Editorial Advisory Board Members:
Francesco Guerra (University of Modena and Reggio Emilia, Italy)
Dickson Lukose (MIMOS, Malaysia)
Diana Maynard (Sheffield University, UK)
John McCrae (University of Bielefeld, Germany)
Frederique Segond (Xerox Research Centere Europe, France)
Michael Uschold (USA)
Ren? Witte (Concordia University, Canada)
Inquiries and submissions can be forwarded electronically (Word document):
Armando Stellato
Department of Computer Science, Systems and Production
University of Rome, Tor Vergata
Tel.: +39 06 7259 7330 ? Fax: +39 06 7259 7460 ? cell: +39 328 9115548
E-mail: stellato at info.uniroma2.it
And in copy to:
Maria Teresa Pazienza: pazienza at info.uniroma2.it
Please send all submissions with the following subject in the mail (copy and
the past it in the subject field of your email to be sure you printed it
correctly)
[IGI-BOOK SAOD | CHAPTER PROPOSAL]
--------------------------------------------------
Ing. Armando Stellato, PhD
AI Research Group,
Dept. of Computer Science, Systems and Production
University of Roma, Tor Vergata
Via del Politecnico 1 00133 ROMA (ITALY)
tel: +39 06 7259 7330 (office, room A1-14);
???? +39 06 7259 7332 (lab)
fax: +39 06 7259 7460
e_mail: stellato at info.uniroma2.it
chat addresses (do not use them for mail, I do not use these addresses for
e-mailing and won't reply to any mail sent to them!)
yahoo: stellato75
jabber(gtalk): stellato75 at gmail.com
skype: odnamar
--------------------------------------------------
From sohaelshafey at yahoo.com Sun Oct 10 07:06:17 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Sun, 10 Oct 2010 07:06:17 -0700 (PDT)
Subject: [protege-discussion] Exception in inference api
Message-ID: <603046.75439.qm@web39603.mail.mud.yahoo.com>
I used protege 4.1 beta build 209 api, and I have a problem in inference api.
This is the snapshot of code that I used to get inferencing:
OWLOntologyManager ontologymanager=OWLManager.createOWLOntologyManager();
??????????? OWLOntology
ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
??????????? OWLDataFactory factory=ontologymanager.getOWLDataFactory();
??????????? OWLReasonerFactory reasonerfactory= new Reasoner.ReasonerFactory();
??????????? OWLReasoner
owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
??????????? owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
?????
List> InferredGenerator = new
ArrayList>();
?????????? InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
?????????? InferredOntologyGenerator ontologygenerator=new
InferredOntologyGenerator(owlreasoner,InferredGenerator);???????????
?????????? ontologygenerator.fillOntology(ontologymanager,ontology);??????
?????????? ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
but I have an exception in this line:
ontologygenerator.fillOntology(ontologymanager,ontology);??
this exception says: java.lang.NullPointerException
?I don't know what i should do and what is wrong.
Thanks in advance
Soha Said
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From tredmond at stanford.edu Sun Oct 10 11:44:48 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Sun, 10 Oct 2010 11:44:48 -0700
Subject: [protege-discussion] Exception in inference api
In-Reply-To: <603046.75439.qm@web39603.mail.mud.yahoo.com>
References: <603046.75439.qm@web39603.mail.mud.yahoo.com>
Message-ID: <4CB209A0.2080207@stanford.edu>
The types of questions you have been asking are better asked on the p4
mailing list as it is about the Protege 4 owl editor. Instructions for
joining that list are here:
http://mailman.stanford.edu/mailman/listinfo/p4-feedback
I used your code pretty much verbatim and did not see the null pointer
exception. In fact the code pretty much did what I expected. I think
that this issue can be cleared up if you supply a bit more information.
> but I have an exception in this line:
> ontologygenerator.fillOntology(ontologymanager,ontology);
> this exception says: java.lang.NullPointerException
> I don't know what i should do and what is wrong.
I suspect that we would know what is wrong immediately if we saw the
exception stack trace. A null pointer that actually thown on that line
would seem to be impossible with the code you sent (based on Java
principles only). The only way to get the null pointer on that line is
if the ontologygenerator variable is null but it is assigned to a
constructed value in the previous line.
So I think that your exception is generated somewhere in code called by
the line
ontologygenerator.fillOntology(ontologymanager,ontology).
Somewhere down inside there something has not been initialized
correctly. An obvious guess is that things went wrong because the
OWLOntology ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
line did not successfully load an ontology. But I (accidentally
actually) tested that and it results in an exception at that line. So I
would guess that this is not the issue either.
I have some other immediate comments on your code.
> I used protege 4.1 beta build 209 api, and I have a problem in
> inference api.
All the code you have supplied is actually based on the Manchester OWL
API (owlapi.sourceforge.net) which is an important library used by
Protege 4.1. I didn't see any Protege specific code in your sample.
In this code there is the line:
OWLReasonerFactory reasonerfactory= new Reasoner.ReasonerFactory();
If you are planning on using this code in Protege 4.1 then this is not
the recommended approach. But your approach may be best for making
quick little applications that you can test before integrating with
Protege 4.1. A better approach if you integrate your code into Protege
4.1 would be something like
OWLReasoner owlreasoner = getOWLModelManager().getReasoner();
if (owlreasoner instanceof NoOpReasoner) {
... tell the user to initialize his reasoner ...
return;
}
else if (!owlreasoner.getPendingChanges().isEmpty()) {
owlreasoner.flush();
}
Most plugin types (view components, menus) will have a
getOWLModelManager() method. I add the reasoner.flush() call here
because I figure that an export inferred axioms operation is
sufficiently expensive that it makes sense to bring the reasoner up to
date first.
Then later you do this step:
owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
It is a good idea to do the precompute step here but you chose the wrong
one for the task that follows. When you create the
InferredOntologyGenerator, you tell it to compute inferred class
assertion axioms (e.g. statements that an individual is in a class).
Precomputing the class hierarchy will not help with this task.
-Timothy
On 10/10/2010 07:06 AM, Soha Said wrote:
> I used protege 4.1 beta build 209 api, and I have a problem in
> inference api.
> This is the snapshot of code that I used to get inferencing:
> OWLOntologyManager ontologymanager=OWLManager.createOWLOntologyManager();
> OWLOntology
> ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> OWLReasonerFactory reasonerfactory= new
> Reasoner.ReasonerFactory();
> OWLReasoner
> owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
>
> owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
>
> List> InferredGenerator =
> new ArrayList>();
> InferredGenerator.add(new
> InferredClassAssertionAxiomGenerator());
> InferredOntologyGenerator ontologygenerator=new
> InferredOntologyGenerator(owlreasoner,InferredGenerator);
> ontologygenerator.fillOntology(ontologymanager,ontology);
> ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> but I have an exception in this line:
> ontologygenerator.fillOntology(ontologymanager,ontology);
> this exception says: java.lang.NullPointerException
> I don't know what i should do and what is wrong.
> Thanks in advance
> Soha Said
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From sohaelshafey at yahoo.com Tue Oct 12 09:28:11 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Tue, 12 Oct 2010 09:28:11 -0700 (PDT)
Subject: [protege-discussion] Exception in inference api
Message-ID: <183994.82904.qm@web39604.mail.mud.yahoo.com>
Hello,
I trace the error and I find the error in this line:
InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
when I replced with this line:
InferredGenerator.add(new InferredPropertyAssertionGenerator());
it worked without error, but when I open the protege, the object properties are
not saved correctly.
for example, each individual will have its object properties and linked to the
other individuals by TopObjectProperty like individual x and y, and x has
TopObjectProperty is y and vise versa.
when i classify from the protege interface, it inferred the properties
correctly, but using api i think there is some problem.
On 10/10/2010 07:06 AM, Soha Said wrote:
> I used protege 4.1 beta build 209 api, and I have a problem in
> inference api.
> This is the snapshot of code that I used to get inferencing:
> OWLOntologyManager ontologymanager=OWLManager.createOWLOntologyManager();
>? ? ? ? ? ? OWLOntology
> ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
>? ? ? ? ? ? OWLDataFactory factory=ontologymanager.getOWLDataFactory();
>? ? ? ? ? ? OWLReasonerFactory reasonerfactory= new
> Reasoner.ReasonerFactory();
>? ? ? ? ? ? OWLReasoner
> owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
>? ? ? ? ? ?
> owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
>
> List> InferredGenerator =
> new ArrayList>();
>? ? ? ? ? ? InferredGenerator.add(new
> InferredClassAssertionAxiomGenerator());
>? ? ? ? ? ? InferredOntologyGenerator ontologygenerator=new
> InferredOntologyGenerator(owlreasoner,InferredGenerator);
>? ? ? ? ? ? ontologygenerator.fillOntology(ontologymanager,ontology);
>? ? ? ? ? ? ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> but I have an exception in this line:
> ontologygenerator.fillOntology(ontologymanager,ontology);
> this exception says: java.lang.NullPointerException
>? I don't know what i should do and what is wrong.
> Thanks in advance
> Soha Said
>
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From tredmond at stanford.edu Tue Oct 12 16:15:30 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 12 Oct 2010 16:15:30 -0700
Subject: [protege-discussion] Exception in inference api
In-Reply-To: <183994.82904.qm@web39604.mail.mud.yahoo.com>
References: <183994.82904.qm@web39604.mail.mud.yahoo.com>
Message-ID: <4CB4EC12.3000004@stanford.edu>
You still did not send the stack trace for your exception. An example
of a stack trace for an exception would be something like this:
java.lang.ClassCastException:
uk.ac.manchester.cs.owl.owlapi.OWLObjectAllValuesFromImpl cannot be cast
to org.semanticweb.owlapi.model.OWLClass
at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
at uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
at uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
at java.util.TreeMap.put(TreeMap.java:562)
at java.util.TreeSet.add(TreeSet.java:255)
at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
Each line in such a trace provides some additional information for a
developer to analyze.
I would say that the API is working because I have modified some code in
Protege 4 recently that looks very much like what you are writing. The
code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
similar to yours.
-Timothy
On 10/12/2010 09:28 AM, Soha Said wrote:
> Hello,
> I trace the error and I find the error in this line:
> InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> when I replced with this line:
> InferredGenerator.add(new InferredPropertyAssertionGenerator());
> it worked without error, but when I open the protege, the object
> properties are not saved correctly.
> for example, each individual will have its object properties and
> linked to the other individuals by TopObjectProperty like individual x
> and y, and x has TopObjectProperty is y and vise versa.
> when i classify from the protege interface, it inferred the properties
> correctly, but using api i think there is some problem.
>
> On 10/10/2010 07:06 AM, Soha Said wrote:
> > I used protege 4.1 beta build 209 api, and I have a problem in
> > inference api.
> > This is the snapshot of code that I used to get inferencing:
> > OWLOntologyManager
> ontologymanager=OWLManager.createOWLOntologyManager();
> > OWLOntology
> > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > OWLReasonerFactory reasonerfactory= new
> > Reasoner.ReasonerFactory();
> > OWLReasoner
> > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> >
> > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> >
> > List> InferredGenerator =
> > new ArrayList>();
> > InferredGenerator.add(new
> > InferredClassAssertionAxiomGenerator());
> > InferredOntologyGenerator ontologygenerator=new
> > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > but I have an exception in this line:
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > this exception says: java.lang.NullPointerException
> > I don't know what i should do and what is wrong.
> > Thanks in advance
> > Soha Said
> >
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From sohaelshafey at yahoo.com Wed Oct 13 15:09:40 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Wed, 13 Oct 2010 15:09:40 -0700 (PDT)
Subject: [protege-discussion] Exception in inference api
Message-ID: <813942.61351.qm@web39604.mail.mud.yahoo.com>
the trace is
java.lang.NullPointerException
at org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown
Source)
at org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
at
org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:46)
at
org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:42)
at
org.semanticweb.owlapi.util.InferredEntityAxiomGenerator.createAxioms(InferredEntityAxiomGenerator.java:49)
at
org.semanticweb.owlapi.util.InferredOntologyGenerator.fillOntology(InferredOntologyGenerator.java:111)
at prototype.PrototypeFrame.InferredInstances(PrototypeFrame.java:898)
at
prototype.PrototypeFrame.BtnInferenceActionPerformed(PrototypeFrame.java:203)
at prototype.PrototypeFrame.access$200(PrototypeFrame.java:36)
at prototype.PrototypeFrame$4.actionPerformed(PrototypeFrame.java:98)
at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6263)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6028)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4630)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4460)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4460)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
-------------------------------------------------------------------------
You still did not send the stack trace for your exception. An example
of a stack trace for an exception would be something like this:
java.lang.ClassCastException:
uk.ac.manchester.cs.owl.owlapi.OWLObjectAllValuesFromImpl cannot be cast
to org.semanticweb.owlapi.model.OWLClass
atuk.ac.manchester.cs.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
at uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
at
uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
at java.util.TreeMap.put(TreeMap.java:562)
at java.util.TreeSet.add(TreeSet.java:255)
at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
Each line in such a trace provides some additional information for a
developer to analyze.
I would say that the API is working because I have modified some code in
Protege 4 recently that looks very much like what you are writing. The
code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
similar to yours.
-Timothy
On 10/12/2010 09:28 AM, Soha Said wrote:
> Hello,
> I trace the error and I find the error in this line:
> InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> when I replced with this line:
> InferredGenerator.add(new InferredPropertyAssertionGenerator());
> it worked without error, but when I open the protege, the object
> properties are not saved correctly.
> for example, each individual will have its object properties and
> linked to the other individuals by TopObjectProperty like individual x
> and y, and x has TopObjectProperty is y and vise versa.
> when i classify from the protege interface, it inferred the properties
> correctly, but using api i think there is some problem.
>
> On 10/10/2010 07:06 AM, Soha Said wrote:
> > I used protege 4.1 beta build 209 api, and I have a problem in
> > inference api.
> > This is the snapshot of code that I used to get inferencing:
> > OWLOntologyManager
> ontologymanager=OWLManager.createOWLOntologyManager();
> > OWLOntology
> > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > OWLReasonerFactory reasonerfactory= new
> > Reasoner.ReasonerFactory();
> > OWLReasoner
> > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> >
> > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> >
> > List> InferredGenerator =
> > new ArrayList>();
> > InferredGenerator.add(new
> > InferredClassAssertionAxiomGenerator());
> > InferredOntologyGenerator ontologygenerator=new
> > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > but I have an exception in this line:
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > this exception says: java.lang.NullPointerException
> > I don't know what i should do and what is wrong.
> > Thanks in advance
> > Soha Said
> >
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From sohaelshafey at yahoo.com Wed Oct 13 15:34:15 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Wed, 13 Oct 2010 15:34:15 -0700 (PDT)
Subject: [protege-discussion] Exception in inference api
Message-ID: <213002.41991.qm@web39607.mail.mud.yahoo.com>
Why using inferrence api from java shows me TopObjectProperty and
TopDataProperty to each individual?
and
This is another the trace from protege when I use classify from reasoner menu
Error 2 Logged at Thu Oct 14 00:29:36 EET 2010
NullPointerException: null
org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown Source)
org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection$1.run(OWLClassAssertionAxiomTypeFrameSection.java:73)
org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:181)
org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection.refillInferred(OWLClassAssertionAxiomTypeFrameSection.java:70)
org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:232)
org.protege.editor.owl.ui.frame.AbstractOWLFrame.refill(AbstractOWLFrame.java:94)
org.protege.editor.owl.ui.frame.AbstractOWLFrame.setRootObject(AbstractOWLFrame.java:86)
org.protege.editor.owl.ui.framelist.OWLFrameList.setRootObject(OWLFrameList.java:349)
org.protege.editor.owl.ui.view.individual.OWLIndividualDescriptionViewComponent.updateView(OWLIndividualDescriptionViewComponent.java:41)
org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:41)
org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:17)
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:194)
org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:72)
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSelectionChanged(OWLSelectionModelImpl.java:192)
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSelectedObject(OWLSelectionModelImpl.java:180)
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedObject(OWLSelectionModelImpl.java:168)
org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedEntity(OWLSelectionModelImpl.java:203)
org.protege.editor.owl.model.OWLWorkspace.verifySelection(OWLWorkspace.java:378)
org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:298)
org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:132)
org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:221)
org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:763)
org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:244)
java.awt.event.InvocationEvent.dispatch(Unknown Source)
java.awt.EventQueue.dispatchEvent(Unknown Source)
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
java.awt.Dialog$1.run(Unknown Source)
java.awt.Dialog$2.run(Unknown Source)
java.security.AccessController.doPrivileged(Native Method)
java.awt.Dialog.show(Unknown Source)
java.awt.Component.show(Unknown Source)
java.awt.Component.setVisible(Unknown Source)
org.protege.editor.owl.ui.inference.ReasonerProgressUI$3.run(ReasonerProgressUI.java:156)
java.awt.event.InvocationEvent.dispatch(Unknown Source)
java.awt.EventQueue.dispatchEvent(Unknown Source)
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
java.awt.EventDispatchThread.pumpEvents(Unknown Source)
java.awt.EventDispatchThread.pumpEvents(Unknown Source)
java.awt.EventDispatchThread.run(Unknown Source)
-----------------------------------------------------------------------------------------------------------------------------
You still did not send the stack trace for your exception. An example
of a stack trace for an exception would be something like this:
java.lang.ClassCastException:
uk.ac.manchester.cs.owl.owlapi.OWLObjectAllValuesFromImpl cannot be cast
to org.semanticweb.owlapi.model.OWLClass
atuk.ac.manchester.cs.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
at uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
at
uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
at java.util.TreeMap.put(TreeMap.java:562)
at java.util.TreeSet.add(TreeSet.java:255)
at uk.ac.manchester.cs.owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
Each line in such a trace provides some additional information for a
developer to analyze.
I would say that the API is working because I have modified some code in
Protege 4 recently that looks very much like what you are writing. The
code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
similar to yours.
-Timothy
On 10/12/2010 09:28 AM, Soha Said wrote:
> Hello,
> I trace the error and I find the error in this line:
> InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> when I replced with this line:
> InferredGenerator.add(new InferredPropertyAssertionGenerator());
> it worked without error, but when I open the protege, the object
> properties are not saved correctly.
> for example, each individual will have its object properties and
> linked to the other individuals by TopObjectProperty like individual x
> and y, and x has TopObjectProperty is y and vise versa.
> when i classify from the protege interface, it inferred the properties
> correctly, but using api i think there is some problem.
>
> On 10/10/2010 07:06 AM, Soha Said wrote:
> > I used protege 4.1 beta build 209 api, and I have a problem in
> > inference api.
> > This is the snapshot of code that I used to get inferencing:
> > OWLOntologyManager
> ontologymanager=OWLManager.createOWLOntologyManager();
> > OWLOntology
> > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > OWLReasonerFactory reasonerfactory= new
> > Reasoner.ReasonerFactory();
> > OWLReasoner
> > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> >
> > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> >
> > List> InferredGenerator =
> > new ArrayList>();
> > InferredGenerator.add(new
> > InferredClassAssertionAxiomGenerator());
> > InferredOntologyGenerator ontologygenerator=new
> > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > but I have an exception in this line:
> > ontologygenerator.fillOntology(ontologymanager,ontology);
> > this exception says: java.lang.NullPointerException
> > I don't know what i should do and what is wrong.
> > Thanks in advance
> > Soha Said
> >
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From tredmond at stanford.edu Wed Oct 13 15:35:58 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Wed, 13 Oct 2010 15:35:58 -0700
Subject: [protege-discussion] Exception in inference api
In-Reply-To: <813942.61351.qm@web39604.mail.mud.yahoo.com>
References: <813942.61351.qm@web39604.mail.mud.yahoo.com>
Message-ID: <4CB6344E.1080903@stanford.edu>
Yes this is much more informative. I was beginning to suspect what was
wrong in your last message. You are using an old version of HermiT. I
remember this exception. I know that this was present in Hermit 1.2.5
but HermiT is now on version 1.3.1.
If you need HermiT outside of Protege, you can obtain it from [1]. If
you are using Protege Build 209, you can update to HermiT by clicking
File->Check For Plugins and then install the HermiT plugin. In the
latter case, I would recommend also updating the OWL editor plugin. I
have recently fixed and improved the export inferred ontology method
which you seem to be using.
I was able to replicate your exception with older versions of HermiT
using the attached ontology.
-Timothy
[1] http://hermit-reasoner.com/
On 10/13/2010 03:09 PM, Soha Said wrote:
> the trace is
> java.lang.NullPointerException
> at
> org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown Source)
> at org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
> at
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:46)
> at
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:42)
> at
> org.semanticweb.owlapi.util.InferredEntityAxiomGenerator.createAxioms(InferredEntityAxiomGenerator.java:49)
> at
> org.semanticweb.owlapi.util.InferredOntologyGenerator.fillOntology(InferredOntologyGenerator.java:111)
> at
> prototype.PrototypeFrame.InferredInstances(PrototypeFrame.java:898)
> at
> prototype.PrototypeFrame.BtnInferenceActionPerformed(PrototypeFrame.java:203)
> at prototype.PrototypeFrame.access$200(PrototypeFrame.java:36)
> at
> prototype.PrototypeFrame$4.actionPerformed(PrototypeFrame.java:98)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> at
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> at java.awt.Component.processMouseEvent(Component.java:6263)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> at java.awt.Component.processEvent(Component.java:6028)
> at java.awt.Container.processEvent(Container.java:2041)
> at java.awt.Component.dispatchEventImpl(Component.java:4630)
> at java.awt.Container.dispatchEventImpl(Container.java:2099)
> at java.awt.Component.dispatchEvent(Component.java:4460)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
> at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
> at
> java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
> at java.awt.Container.dispatchEventImpl(Container.java:2085)
> at java.awt.Window.dispatchEventImpl(Window.java:2478)
> at java.awt.Component.dispatchEvent(Component.java:4460)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
> -------------------------------------------------------------------------
> You still did not send the stack trace for your exception. An example
> of a stack trace for an exception would be something like this:
>
> java.lang.ClassCastException:
> uk.ac.manchester.cs
> .owl.owlapi.OWLObjectAllValuesFromImpl
> cannot be cast
> to org.semanticweb.owlapi.model.OWLClass
> atuk.ac.manchester.cs
> .owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
> at uk.ac.manchester.cs
> .owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
> at
> uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
> at java.util.TreeMap.put(TreeMap.java:562)
> at java.util.TreeSet.add(TreeSet.java:255)
> at uk.ac.manchester.cs
> .owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
>
>
>
> Each line in such a trace provides some additional information for a
> developer to analyze.
>
> I would say that the API is working because I have modified some code in
> Protege 4 recently that looks very much like what you are writing. The
> code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
> similar to yours.
>
> -Timothy
>
>
> On 10/12/2010 09:28 AM, Soha Said wrote:
> > Hello,
> > I trace the error and I find the error in this line:
> > InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> > when I replced with this line:
> > InferredGenerator.add(new InferredPropertyAssertionGenerator());
> > it worked without error, but when I open the protege, the object
> > properties are not saved correctly.
> > for example, each individual will have its object properties and
> > linked to the other individuals by TopObjectProperty like individual x
> > and y, and x has TopObjectProperty is y and vise versa.
> > when i classify from the protege interface, it inferred the properties
> > correctly, but using api i think there is some problem.
> >
> > On 10/10/2010 07:06 AM, Soha Said wrote:
> > > I used protege 4.1 beta build 209 api, and I have a problem in
> > > inference api.
> > > This is the snapshot of code that I used to get inferencing:
> > > OWLOntologyManager
> > ontologymanager=OWLManager.createOWLOntologyManager();
> > > OWLOntology
> > > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > > OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > > OWLReasonerFactory reasonerfactory= new
> > > Reasoner.ReasonerFactory();
> > > OWLReasoner
> > > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> > >
> > > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> > >
> > > List> InferredGenerator =
> > > new ArrayList>();
> > > InferredGenerator.add(new
> > > InferredClassAssertionAxiomGenerator());
> > > InferredOntologyGenerator ontologygenerator=new
> > > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > > but I have an exception in this line:
> > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > this exception says: java.lang.NullPointerException
> > > I don't know what i should do and what is wrong.
> > > Thanks in advance
> > > Soha Said
> > >
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From tredmond at stanford.edu Wed Oct 13 15:50:49 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Wed, 13 Oct 2010 15:50:49 -0700
Subject: [protege-discussion] Exception in inference api
In-Reply-To: <213002.41991.qm@web39607.mail.mud.yahoo.com>
References: <213002.41991.qm@web39607.mail.mud.yahoo.com>
Message-ID: <4CB637C9.4010406@stanford.edu>
On 10/13/2010 03:34 PM, Soha Said wrote:
>
> Why using inferrence api from java shows me TopObjectProperty and
> TopDataProperty to each individual?
I didn't see that in my copy of Protege but I believe it. I have been
on a mission to remove the trivial inferred facts from the display.
There have been several and I keep finding more. So for instance it
used to be that a Protege would show owl:Thing for a class without an
asserted parent. It also used to show that that the inferred domain of
a property is owl:Thing if no better domain was known.
These types of inferred facts are true but they are not interesting. I
have just found another one (Protege shows that individuals without an
explicit type are of type owl:Thing).
-Timothy
> and
> This is another the trace from protege when I use classify from
> reasoner menu
>
> Error 2 Logged at Thu Oct 14 00:29:36 EET 2010
> NullPointerException: null
> org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown
> Source)
> org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
>
> org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection$1.run(OWLClassAssertionAxiomTypeFrameSection.java:73)
>
> org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask(ReasonerPreferences.java:181)
>
> org.protege.editor.owl.ui.frame.individual.OWLClassAssertionAxiomTypeFrameSection.refillInferred(OWLClassAssertionAxiomTypeFrameSection.java:70)
>
> org.protege.editor.owl.ui.frame.AbstractOWLFrameSection.setRootObject(AbstractOWLFrameSection.java:232)
>
> org.protege.editor.owl.ui.frame.AbstractOWLFrame.refill(AbstractOWLFrame.java:94)
>
> org.protege.editor.owl.ui.frame.AbstractOWLFrame.setRootObject(AbstractOWLFrame.java:86)
>
> org.protege.editor.owl.ui.framelist.OWLFrameList.setRootObject(OWLFrameList.java:349)
>
> org.protege.editor.owl.ui.view.individual.OWLIndividualDescriptionViewComponent.updateView(OWLIndividualDescriptionViewComponent.java:41)
>
> org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:41)
>
> org.protege.editor.owl.ui.view.individual.AbstractOWLIndividualViewComponent.updateView(AbstractOWLIndividualViewComponent.java:17)
>
> org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent.updateViewContentAndHeader(AbstractOWLSelectionViewComponent.java:194)
>
> org.protege.editor.owl.ui.view.AbstractOWLSelectionViewComponent$1.selectionChanged(AbstractOWLSelectionViewComponent.java:72)
>
> org.protege.editor.owl.model.selection.OWLSelectionModelImpl.fireSelectionChanged(OWLSelectionModelImpl.java:192)
>
> org.protege.editor.owl.model.selection.OWLSelectionModelImpl.updateSelectedObject(OWLSelectionModelImpl.java:180)
>
> org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedObject(OWLSelectionModelImpl.java:168)
>
> org.protege.editor.owl.model.selection.OWLSelectionModelImpl.setSelectedEntity(OWLSelectionModelImpl.java:203)
>
> org.protege.editor.owl.model.OWLWorkspace.verifySelection(OWLWorkspace.java:378)
>
> org.protege.editor.owl.model.OWLWorkspace.handleModelManagerEvent(OWLWorkspace.java:298)
>
> org.protege.editor.owl.model.OWLWorkspace.access$000(OWLWorkspace.java:132)
>
> org.protege.editor.owl.model.OWLWorkspace$1.handleChange(OWLWorkspace.java:221)
>
> org.protege.editor.owl.model.OWLModelManagerImpl.fireEvent(OWLModelManagerImpl.java:763)
>
> org.protege.editor.owl.model.inference.OWLReasonerManagerImpl$2.run(OWLReasonerManagerImpl.java:244)
> java.awt.event.InvocationEvent.dispatch(Unknown Source)
> java.awt.EventQueue.dispatchEvent(Unknown Source)
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> java.awt.Dialog$1.run(Unknown Source)
> java.awt.Dialog$2.run(Unknown Source)
> java.security.AccessController.doPrivileged(Native Method)
> java.awt.Dialog.show(Unknown Source)
> java.awt.Component.show(Unknown Source)
> java.awt.Component.setVisible(Unknown Source)
>
> org.protege.editor.owl.ui.inference.ReasonerProgressUI$3.run(ReasonerProgressUI.java:156)
> java.awt.event.InvocationEvent.dispatch(Unknown Source)
> java.awt.EventQueue.dispatchEvent(Unknown Source)
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> java.awt.EventDispatchThread.run(Unknown Source)
> -----------------------------------------------------------------------------------------------------------------------------
>
> You still did not send the stack trace for your exception. An example
> of a stack trace for an exception would be something like this:
>
> java.lang.ClassCastException:
> uk.ac.manchester.cs
> .owl.owlapi.OWLObjectAllValuesFromImpl
> cannot be cast
> to org.semanticweb.owlapi.model.OWLClass
> atuk.ac.manchester.cs
> .owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
> at uk.ac.manchester.cs
> .owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
> at
> uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
> at java.util.TreeMap.put(TreeMap.java:562)
> at java.util.TreeSet.add(TreeSet.java:255)
> at uk.ac.manchester.cs
> .owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
>
>
>
> Each line in such a trace provides some additional information for a
> developer to analyze.
>
> I would say that the API is working because I have modified some code in
> Protege 4 recently that looks very much like what you are writing. The
> code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
> similar to yours.
>
> -Timothy
>
>
> On 10/12/2010 09:28 AM, Soha Said wrote:
> > Hello,
> > I trace the error and I find the error in this line:
> > InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> > when I replced with this line:
> > InferredGenerator.add(new InferredPropertyAssertionGenerator());
> > it worked without error, but when I open the protege, the object
> > properties are not saved correctly.
> > for example, each individual will have its object properties and
> > linked to the other individuals by TopObjectProperty like individual x
> > and y, and x has TopObjectProperty is y and vise versa.
> > when i classify from the protege interface, it inferred the properties
> > correctly, but using api i think there is some problem.
> >
> > On 10/10/2010 07:06 AM, Soha Said wrote:
> > > I used protege 4.1 beta build 209 api, and I have a problem in
> > > inference api.
> > > This is the snapshot of code that I used to get inferencing:
> > > OWLOntologyManager
> > ontologymanager=OWLManager.createOWLOntologyManager();
> > > OWLOntology
> > > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > > OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > > OWLReasonerFactory reasonerfactory= new
> > > Reasoner.ReasonerFactory();
> > > OWLReasoner
> > > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> > >
> > > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> > >
> > > List> InferredGenerator =
> > > new ArrayList>();
> > > InferredGenerator.add(new
> > > InferredClassAssertionAxiomGenerator());
> > > InferredOntologyGenerator ontologygenerator=new
> > > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > > but I have an exception in this line:
> > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > this exception says: java.lang.NullPointerException
> > > I don't know what i should do and what is wrong.
> > > Thanks in advance
> > > Soha Said
> > >
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From sohaelshafey at yahoo.com Wed Oct 13 16:03:48 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Wed, 13 Oct 2010 16:03:48 -0700 (PDT)
Subject: [protege-discussion] [SPAM:##] Re: Exception in inference api
Message-ID: <22047_1287011030_4CB63AD5_22047_11824_1_468734.71000.qm@web39605.mail.mud.yahoo.com>
Yes, Done with no error
Thanks very much
But about topobjectproperty and topDataproperty
how can I avoid it.
Also, object properties inferred correctly from protege interface
but not inferred using api
It was working correct in previous version and data properties not and now vise
versa.
------------------------------------------------
Yes this is much more informative.? I was beginning to suspect what was
wrong in your last message.? You are using an old version of HermiT.? I
remember this exception.? I know that this was present in Hermit 1.2.5
but HermiT is now on version 1.3.1.
If you need HermiT outside of Protege, you can obtain it from [1].? If
you are using Protege Build 209, you can update to HermiT by clicking
File->Check For Plugins and then install the HermiT plugin.? In the
latter case, I would recommend also updating the OWL editor plugin.? I
have recently fixed and improved the export inferred ontology method
which you seem to be using.
I was able to replicate your exception with older versions of HermiT
using the attached ontology.
-Timothy
[1] http://hermit-reasoner.com/
On 10/13/2010 03:09 PM, Soha Said wrote:
> the trace is
> java.lang.NullPointerException
>? ? ? ? at
> org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown Source)
>? ? ? ? at org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
>? ? ? ? at
>org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:46)
>)
>? ? ? ? at
>org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:42)
>)
>? ? ? ? at
>org.semanticweb.owlapi.util.InferredEntityAxiomGenerator.createAxioms(InferredEntityAxiomGenerator.java:49)
>)
>? ? ? ? at
>org.semanticweb.owlapi.util.InferredOntologyGenerator.fillOntology(InferredOntologyGenerator.java:111)
>)
>? ? ? ? at
> prototype.PrototypeFrame.InferredInstances(PrototypeFrame.java:898)
>? ? ? ? at
> prototype.PrototypeFrame.BtnInferenceActionPerformed(PrototypeFrame.java:203)
>? ? ? ? at prototype.PrototypeFrame.access$200(PrototypeFrame.java:36)
>? ? ? ? at
> prototype.PrototypeFrame$4.actionPerformed(PrototypeFrame.java:98)
>? ? ? ? at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
>? ? ? ? at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
>? ? ? ? at
>
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
>? ? ? ? at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
>? ? ? ? at
>javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
>)
>? ? ? ? at java.awt.Component.processMouseEvent(Component.java:6263)
>? ? ? ? at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
>? ? ? ? at java.awt.Component.processEvent(Component.java:6028)
>? ? ? ? at java.awt.Container.processEvent(Container.java:2041)
>? ? ? ? at java.awt.Component.dispatchEventImpl(Component.java:4630)
>? ? ? ? at java.awt.Container.dispatchEventImpl(Container.java:2099)
>? ? ? ? at java.awt.Component.dispatchEvent(Component.java:4460)
>? ? ? ? at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
>? ? ? ? at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
>? ? ? ? at
> java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
>? ? ? ? at java.awt.Container.dispatchEventImpl(Container.java:2085)
>? ? ? ? at java.awt.Window.dispatchEventImpl(Window.java:2478)
>? ? ? ? at java.awt.Component.dispatchEvent(Component.java:4460)
>? ? ? ? at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
>? ? ? ? at
>java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
>)
>? ? ? ? at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
>? ? ? ? at
>java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
>)
>? ? ? ? at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
>? ? ? ? at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
>? ? ? ? at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
> -------------------------------------------------------------------------
> You still did not send the stack trace for your exception.? An example
> of a stack trace for an exception would be something like this:
>
>? ? java.lang.ClassCastException:
> uk.ac.manchester.cs
> .owl.owlapi.OWLObjectAllValuesFromImpl
> cannot be cast
>? ? ? to org.semanticweb.owlapi.model.OWLClass
>? ? ? atuk.ac.manchester.cs
>.owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
>)
>? ? ? at uk.ac.manchester.cs
>.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
>)
>? ? ? at
> uk.ac.manchester.cs.owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
>? ? ? at java.util.TreeMap.put(TreeMap.java:562)
>? ? ? at java.util.TreeSet.add(TreeSet.java:255)
>? ? ? at uk.ac.manchester.cs
>.owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
>)
>
>
>
> Each line in such a trace provides some additional information for a
> developer to analyze.
>
> I would say that the API is working because I have modified some code in
> Protege 4 recently that looks very much like what you are writing.? The
> code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
> similar to yours.
>
> -Timothy
>
>
> On 10/12/2010 09:28 AM, Soha Said wrote:
> > Hello,
> > I trace the error and I find the error in this line:
> > InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> > when I replced with this line:
> > InferredGenerator.add(new InferredPropertyAssertionGenerator());
> > it worked without error, but when I open the protege, the object
> > properties are not saved correctly.
> > for example, each individual will have its object properties and
> > linked to the other individuals by TopObjectProperty like individual x
> > and y, and x has TopObjectProperty is y and vise versa.
> > when i classify from the protege interface, it inferred the properties
> > correctly, but using api i think there is some problem.
> >
> > On 10/10/2010 07:06 AM, Soha Said wrote:
> > > I used protege 4.1 beta build 209 api, and I have a problem in
> > > inference api.
> > > This is the snapshot of code that I used to get inferencing:
> > > OWLOntologyManager
> > ontologymanager=OWLManager.createOWLOntologyManager();
> > >? ? ? ? ? ? OWLOntology
> > > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > >? ? ? ? ? ? OWLDataFactory factory=ontologymanager.getOWLDataFactory();
> > >? ? ? ? ? ? OWLReasonerFactory reasonerfactory= new
> > > Reasoner.ReasonerFactory();
> > >? ? ? ? ? ? OWLReasoner
> > > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> > >
> > > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> > >
> > > List> InferredGenerator =
> > > new ArrayList>();
> > >? ? ? ? ? ? InferredGenerator.add(new
> > > InferredClassAssertionAxiomGenerator());
> > >? ? ? ? ? ? InferredOntologyGenerator ontologygenerator=new
> > > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > >? ? ? ? ? ? ontologygenerator.fillOntology(ontologymanager,ontology);
> > >? ? ? ? ? ? ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > > but I have an exception in this line:
> > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > this exception says: java.lang.NullPointerException
> > >? I don't know what i should do and what is wrong.
> > > Thanks in advance
> > > Soha Said
> > >
>
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From liukzg at gmail.com Fri Oct 15 07:47:57 2010
From: liukzg at gmail.com (=?GB2312?B?wfW/tQ==?=)
Date: Fri, 15 Oct 2010 22:47:57 +0800
Subject: [protege-discussion] Why my applet can't run in explore
Message-ID:
I have write a OWL applet with jena and pellet, it works in the eclipse, but
can't do in explore.The error's imformations as bellow:
java.lang.RuntimeException: java.lang.NoClassDefFoundError:
com/hp/hpl/jena/rdf/model/Resource
at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
at
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NoClassDefFoundError:
com/hp/hpl/jena/rdf/model/Resource
at FunctionApplet.(FunctionApplet.java:14)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown
Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance0(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at sun.plugin2.applet.Plugin2Manager$12.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException:
com.hp.hpl.jena.rdf.model.Resource
at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
at sun.plugin2.applet.Plugin2ClassLoader.loadClass0(Unknown Source)
at sun.plugin2.applet.Plugin2ClassLoader.loadClass(Unknown Source)
at sun.plugin2.applet.Plugin2ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 16 more
Caused by: java.io.FileNotFoundException:
F:\LK\??\java\FunctionOWL\bin\com\hp\hpl\jena\rdf\model\Resource.class
(???????????)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(Unknown Source)
at java.io.FileInputStream.(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.connect(Unknown
Source)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown
Source)
at sun.plugin2.applet.Applet2ClassLoader.getBytes(Unknown Source)
at sun.plugin2.applet.Applet2ClassLoader.access$000(Unknown Source)
at sun.plugin2.applet.Applet2ClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
... 21 more
Could you tell me why?
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From tredmond at stanford.edu Fri Oct 15 08:08:43 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Fri, 15 Oct 2010 08:08:43 -0700
Subject: [protege-discussion] Why my applet can't run in explore
In-Reply-To:
References:
Message-ID: <4CB86E7B.4010706@stanford.edu>
On 10/15/2010 07:47 AM, ?? wrote:
> I have write a OWL applet with jena and pellet, it works in the
> eclipse, but can't do in explore.The error's imformations as bellow:
>
You have some type of configuration problem in your applet. The jena jar
is not on the classpath. Debugging applets can be difficult actually but
in this case you are doing well because you see the exception.
-Timothy
> java.lang.RuntimeException: java.lang.NoClassDefFoundError:
> com/hp/hpl/jena/rdf/model/Resource
>
> at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
>
> at
> sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
> Source)
>
> at java.lang.Thread.run(Unknown Source)
>
> Caused by: java.lang.NoClassDefFoundError:
> com/hp/hpl/jena/rdf/model/Resource
>
> at FunctionApplet.(FunctionApplet.java:14)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
>
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
> Source)
>
> at java.lang.reflect.Constructor.newInstance(Unknown Source)
>
> at java.lang.Class.newInstance0(Unknown Source)
>
> at java.lang.Class.newInstance(Unknown Source)
>
> at sun.plugin2.applet.Plugin2Manager$12.run(Unknown Source)
>
> at java.awt.event.InvocationEvent.dispatch(Unknown Source)
>
> at java.awt.EventQueue.dispatchEvent(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>
> at java.awt.EventDispatchThread.run(Unknown Source)
>
> Caused by: java.lang.ClassNotFoundException:
> com.hp.hpl.jena.rdf.model.Resource
>
> at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
>
> at sun.plugin2.applet.Plugin2ClassLoader.loadClass0(Unknown Source)
>
> at sun.plugin2.applet.Plugin2ClassLoader.loadClass(Unknown Source)
>
> at sun.plugin2.applet.Plugin2ClassLoader.loadClass(Unknown Source)
>
> at java.lang.ClassLoader.loadClass(Unknown Source)
>
> ... 16 more
>
> Caused by: java.io.FileNotFoundException: F:\LK\??\java\FunctionOWL
> \bin\com\hp\hpl\jena\rdf\model\Resource.class (???????????)
>
> at java.io.FileInputStream.open(Native Method)
>
> at java.io.FileInputStream.(Unknown Source)
>
> at java.io.FileInputStream.(Unknown Source)
>
> at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
>
> at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown
> Source)
>
> at sun.plugin2.applet.Applet2ClassLoader.getBytes(Unknown Source)
>
> at sun.plugin2.applet.Applet2ClassLoader.access$000(Unknown Source)
>
> at sun.plugin2.applet.Applet2ClassLoader$1.run(Unknown Source)
>
> at java.security.AccessController.doPrivileged(Native Method)
>
> ... 21 more
>
> Could you tell me why?
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From tudorache at stanford.edu Fri Oct 15 15:40:08 2010
From: tudorache at stanford.edu (Tania Tudorache)
Date: Fri, 15 Oct 2010 15:40:08 -0700
Subject: [protege-discussion] Postdoc position on "Next Generation Ontology
Authoring Tools" available at Univ. of Victoria
Message-ID: <4CB8D848.5080306@stanford.edu>
Online version:
http://www.thechiselgroup.org/files/uploads/Opening%20postdoc%20ncbo.pdf
Opening: Post-doctoral Research Position
The CHISEL Group, Department of Computer Science, University of Victoria
Topic: Next Generation Ontology Authoring Tools
========================================================
The CHISEL (Computer Human Interaction for Software Engineering) group
at the
University of Victoria is seeking applications for a post-doctoral
position on Next
Generation Ontology Authoring Tools, starting January 2011 (or sooner if
available).
Our research group is a highly motivated group of students and faculty
that enjoy working
within a collaborative research environment with strong connections to
industry. Details
on some of our current and previous projects can be found at
www.thechiselgroup.org.
This two year position, renewable for up to 5 years, is supported by a
grant from the
National Institute of Health for a ?National Center on Biomedical
Computing? (see
http://www.bioontology.org/). This project is a close collaboration with
Stanford University.
Your role will be to participate in empirical studies and in the design
of novel tools to
support the National Center on Biomedical Computing. You should have a
PhD and
publications in knowledge engineering, software engineering, or related
fields.
Background in one or more of the following areas is highly desirable:
knowledge
engineering, social media, software engineering, computer supported
cooperative work,
empirical research, statistics, human computer interaction, and
information visualization.
You should have strong communication skills in English, desire to work
as part of a team,
and a willingness to help PhD and Masters students with their research.
There are no
teaching duties associated with this position, but opportunities to
teach can be negotiated.
The salary for this position is highly competitive and includes full
benefits. Applicants
that apply before Nov 3rd 2010 may also wish to consider applying for a
Banting
Postdoctoral Fellowship (see
http://banting.fellowships-bourses.gc.ca/home-accueil-
eng.html). Additional top-up to this grant would be available.
Applicants should email a curriculum vitae, list of publications, a list
of three referees and
short summary of your research interests to: Prof. Margaret-Anne Storey,
mstorey at uvic.ca.
Requests for more information and clarifications are welcome and should be
sent by email to mstorey at uvic.ca .
The University of Victoria is an equity employer and encourages
applications from women, persons
with disabilities, visible minorities, Aboriginal Peoples, people of all
sexual orientations and
genders, and others who may contribute to the further diversification of
the University.
All qualified candidates are encouraged to apply; however, in accordance
with Canadian
Immigration requirements, Canadians and permanent residents will be
given priority.
From liukzg at gmail.com Fri Oct 15 17:44:40 2010
From: liukzg at gmail.com (=?GB2312?B?wfW/tQ==?=)
Date: Sat, 16 Oct 2010 08:44:40 +0800
Subject: [protege-discussion] Why my applet can't run in explore
In-Reply-To: <4CB86E7B.4010706@stanford.edu>
References:
<4CB86E7B.4010706@stanford.edu>
Message-ID:
Hi, thank your help.
I have put the jena.jar and pellet.jar on the dictionary, and add them to
the "archive=...". It seem the pakage is ok now, but the errors exist remain
as follow:
----------------------------------------------------
java.lang.RuntimeException: java.lang.ExceptionInInitializerError
at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
at
sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ExceptionInInitializerError
at
com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:119)
at
com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:113)
at
com.hp.hpl.jena.rdf.model.impl.ModelSpecImpl.(ModelSpecImpl.java:56)
at
org.mindswap.pellet.jena.PelletReasonerFactory.(PelletReasonerFactory.java:51)
at JenaOWL.JenaOWLTool.(JenaOWLTool.java:43)
at JenaOWL.FuncJenaOWL.(FuncJenaOWL.java:11)
........
-------------------------------------------------------
According to the errors, the jena's createDefaultModel, or the ModelFactory
is not work. I don't know why? It works ok in eclipse. I use the
pellet-1.4-RC1, and the package of pellet.jar is the one of in it's
pellet-1.4-RC1/lib, the jena.jar is the one of in the
pellet-1.4-RC1/lib/jena. Is there any mistake?
? 2010?10?15? ??11:08?Timothy Redmond ???
> On 10/15/2010 07:47 AM, ?? wrote:
>
> I have write a OWL applet with jena and pellet, it works in the eclipse,
> but can't do in explore.The error's imformations as bellow:
>
> You have some type of configuration problem in your applet. The jena jar
> is not on the classpath. Debugging applets can be difficult actually but in
> this case you are doing well because you see the exception.
>
> -Timothy
>
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From tredmond at stanford.edu Sat Oct 16 20:14:15 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Sat, 16 Oct 2010 20:14:15 -0700
Subject: [protege-discussion] Why my applet can't run in explore
In-Reply-To:
References: <4CB86E7B.4010706@stanford.edu>
Message-ID: <4CBA6A07.1070700@stanford.edu>
You are getting into more difficult errors. Is there no other caused by
further down in the stack trace? It can be difficult to get an applet
working because the policy for applets is pretty stringent.
-Timothy
On 10/15/2010 05:44 PM, ?? wrote:
> Hi, thank your help.
> I have put the jena.jar and pellet.jar on the dictionary, and add them
> to the "archive=...". It seem the pakage is ok now, but the errors
> exist remain as follow:
> ----------------------------------------------------
>
> java.lang.RuntimeException: java.lang.ExceptionInInitializerError
>
> at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
>
> at
> sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
> Source)
>
> at java.lang.Thread.run(Unknown Source)
>
> Caused by: java.lang.ExceptionInInitializerError
>
> at
> com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:119)
>
> at
> com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:113)
>
> at
> com.hp.hpl.jena.rdf.model.impl.ModelSpecImpl.(ModelSpecImpl.java:56)
>
> at
> org.mindswap.pellet.jena.PelletReasonerFactory.(PelletReasonerFactory.java:51)
>
> at JenaOWL.JenaOWLTool.(JenaOWLTool.java:43)
>
> at JenaOWL.FuncJenaOWL.(FuncJenaOWL.java:11)
>
> ........
> -------------------------------------------------------
> According to the errors, the jena's createDefaultModel, or the
> ModelFactory is not work. I don't know why? It works ok in eclipse. I
> use the pellet-1.4-RC1, and the package of pellet.jar is the one of in
> it's pellet-1.4-RC1/lib, the jena.jar is the one of in the
> pellet-1.4-RC1/lib/jena. Is there any mistake?
>
> ? 2010?10?15? ??11:08?Timothy Redmond >???
>
> On 10/15/2010 07:47 AM, ?? wrote:
>> I have write a OWL applet with jena and pellet, it works in the
>> eclipse, but can't do in explore.The error's imformations as bellow:
>>
> You have some type of configuration problem in your applet. The
> jena jar is not on the classpath. Debugging applets can be
> difficult actually but in this case you are doing well because you
> see the exception.
>
> -Timothy
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From plwhetzel at gmail.com Sat Oct 16 23:25:35 2010
From: plwhetzel at gmail.com (Trish Whetzel)
Date: Sat, 16 Oct 2010 23:25:35 -0700
Subject: [protege-discussion] NCBO Webinar - James Geller,
October 20 at 10:00am PT
In-Reply-To:
References:
Message-ID:
The next NCBO Webinar will be presented by Dr. James Geller from the New
Jersey Institute of Technology on "The Neighborhood Auditing Tool for the
UMLS and its Source Terminologies" at 10:00am PDT, Wednesday, October 20.
Below is information on how to join the online meeting via WebEx and
accompanying teleconference. Please note there will not be a VOIP option and
attendees must call into the teleconference. For the full schedule of the
NCBO Webinar presentations see: http://www.bioontology.org/webinar-series.
ABSTRACT:
The UMLS's integration of more than 100 source vocabularies makes it
susceptible to errors. Furthermore, its size and complexity can make it
very difficult to locate such errors. A software tool, called the
Neighborhood Auditing Tool (NAT), that facilitates UMLS auditing is
presented. The NAT supports "neighborhood-based" auditing, where, at any
given time, an auditor concentrates on a single focus concept and one of a
variety of neighborhoods of its closely related concepts. The NAT can be
seen as a special browser for the complex structure of the UMLS's
hierarchies. Typical diagrammatic displays of concept networks have a
number of shortcomings, so the NAT utilizes a hybrid diagram/text interface
that features stylized neighborhood views which retain some of the best
features of both the diagrammatic layouts and text windows while avoiding
the shortcomings. The NAT allows an auditor to display knowledge from both
the Metathesaurus (concept) level and the Semantic Network (semantic type)
level. Various additional features of the NAT that support the auditing
process are described. The usefulness of the NAT is demonstrated through a
group of case studies. Its impact is tested with a study involving a select
group of auditors.
BIO:
Dr. James Geller received an Electrical Engineering Diploma from the
Technical University, Vienna, Austria, in 1979, and the MS Degree (1984) and
Ph.D. degree (1988) in Computer Science from the State University of New
York at Buffalo. Dr. Geller joined the Computer Science Department of the
New Jersey Institute of Technology (NJIT) in 1988. He was granted tenure and
promoted to associate professor in 1993. Subsequently he was promoted to
full professor in 2000. Dr. Geller has authored and co-authored about forty
journal papers and over fifty conference papers. These papers are in a
number of areas, including Knowledge Representation, the Semantic Web,
Semantic Modeling in Object-Oriented Databases, Web Mining, Medical
Informatics, Medical Vocabularies, and Auditing of Ontologies and Medical
Terminologies.
WEBEX DETAILS:
Topic: NCBO Webinar Series
Date: Wednesday, October 20, 2010
Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00)
Meeting Number: 929 613 752
Meeting Password: ncbomeeting
-------------------------------------------------------
To join the online meeting (Now from the Apple iPhone (R) and other
smartphones!)
-------------------------------------------------------
1. Go to
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From perisbrodsky2011 at u.northwestern.edu Sun Oct 17 07:16:35 2010
From: perisbrodsky2011 at u.northwestern.edu (Peris Brodsky)
Date: Sun, 17 Oct 2010 09:16:35 -0500
Subject: [protege-discussion] Why my applet can't run in explore
In-Reply-To: <4CBA6A07.1070700@stanford.edu>
References:
<4CB86E7B.4010706@stanford.edu>
<4CBA6A07.1070700@stanford.edu>
Message-ID:
I've worked a lot at getting an applet to work recently, so maybe I can
help. The sandbox does have a lot of limitations, but with those you will
see some kind of Security or Access Exception thrown. The full stack trace
would help.
Specifically with IE, I had problems with it accepting servlet session
cookies from the applet. Worked fine with every other browser. I gave up
and wrote my own session implementation, since the server was mine to
rewrite. Your mileage may vary.
-Peris
2010/10/16 Timothy Redmond
>
> You are getting into more difficult errors. Is there no other caused by
> further down in the stack trace? It can be difficult to get an applet
> working because the policy for applets is pretty stringent.
>
> -Timothy
>
>
>
>
> On 10/15/2010 05:44 PM, ?? wrote:
>
> Hi, thank your help.
> I have put the jena.jar and pellet.jar on the dictionary, and add them to
> the "archive=...". It seem the pakage is ok now, but the errors exist remain
> as follow:
> ----------------------------------------------------
>
> java.lang.RuntimeException: java.lang.ExceptionInInitializerError
>
> at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
>
> at
> sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown
> Source)
>
> at java.lang.Thread.run(Unknown Source)
>
> Caused by: java.lang.ExceptionInInitializerError
>
> at
> com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:119)
>
> at
> com.hp.hpl.jena.rdf.model.ModelFactory.createDefaultModel(ModelFactory.java:113)
>
> at
> com.hp.hpl.jena.rdf.model.impl.ModelSpecImpl.(ModelSpecImpl.java:56)
>
> at
> org.mindswap.pellet.jena.PelletReasonerFactory.(PelletReasonerFactory.java:51)
>
> at JenaOWL.JenaOWLTool.(JenaOWLTool.java:43)
>
> at JenaOWL.FuncJenaOWL.(FuncJenaOWL.java:11)
> ........
> -------------------------------------------------------
> According to the errors, the jena's createDefaultModel, or the ModelFactory
> is not work. I don't know why? It works ok in eclipse. I use the
> pellet-1.4-RC1, and the package of pellet.jar is the one of in it's
> pellet-1.4-RC1/lib, the jena.jar is the one of in the
> pellet-1.4-RC1/lib/jena. Is there any mistake?
>
> ? 2010?10?15? ??11:08?Timothy Redmond ? ??
>
>> On 10/15/2010 07:47 AM, ?? wrote:
>>
>> I have write a OWL applet with jena and pellet, it works in the eclipse,
>> but can't do in explore.The error's imformations as bellow:
>>
>> You have some type of configuration problem in your applet. The jena
>> jar is not on the classpath. Debugging applets can be difficult actually
>> but in this case you are doing well because you see the exception.
>>
>> -Timothy
>>
>
>
> _______________________________________________
> protege-discussion mailing listprotege-discussion at lists.stanford.eduhttps://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
--
?Ah, but a man's reach should exceed his grasp, or what's a heaven for??
--Robert Browning
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From tredmond at stanford.edu Sun Oct 17 10:31:53 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Sun, 17 Oct 2010 10:31:53 -0700
Subject: [protege-discussion] [SPAM:##] Re: Exception in inference api
In-Reply-To: <22047_1287011030_4CB63AD5_22047_11824_1_468734.71000.qm@web39605.mail.mud.yahoo.com>
References: <22047_1287011030_4CB63AD5_22047_11824_1_468734.71000.qm@web39605.mail.mud.yahoo.com>
Message-ID: <4CBB3309.4070001@stanford.edu>
On 10/13/2010 04:03 PM, Soha Said wrote:
> Yes, Done with no error
> Thanks very much
> But about topobjectproperty and topDataproperty
> how can I avoid it.
Here I don't know what you mean. If you are talking about an issue in
Protege then this is my problem. Check that it happens with the latest
release and the latest updates (File->Check for Plugins), report it so
that I can repeat the problem here and I will remove the inference.
If you are talking about a problem in your code then you simply need to
adjust. If some of the inferences being generated by the reasoner are
too trivial and you don't want to see them, then you can programatically
remove the information that you don't want to see.
> Also, object properties inferred correctly from protege interface
> but not inferred using api
All of the details are missing here so it is hard to know what you
mean. It is clear that some code is not behaving as you expect. The
best way to report such an issue is to send a small example which does
not have the desired behavior and explain what you think it is doing
wrong. Preferably you will be working with the latest version of the
software because it is not clear what to do with a bug report about
something that has already been fixed. The very best bug reports
include enough information that the issue can be easily replicated here.
-Timothy
> It was working correct in previous version and data properties not and
> now vise versa.
> ------------------------------------------------
> Yes this is much more informative. I was beginning to suspect what was
> wrong in your last message. You are using an old version of HermiT. I
> remember this exception. I know that this was present in Hermit 1.2.5
> but HermiT is now on version 1.3.1.
>
> If you need HermiT outside of Protege, you can obtain it from [1]. If
> you are using Protege Build 209, you can update to HermiT by clicking
> File->Check For Plugins and then install the HermiT plugin. In the
> latter case, I would recommend also updating the OWL editor plugin. I
> have recently fixed and improved the export inferred ontology method
> which you seem to be using.
>
> I was able to replicate your exception with older versions of HermiT
> using the attached ontology.
>
> -Timothy
>
> [1] http://hermit-reasoner.com/
>
>
> On 10/13/2010 03:09 PM, Soha Said wrote:
> > the trace is
> > java.lang.NullPointerException
> > at
> > org.semanticweb.HermiT.hierarchy.InstanceManager.getTypes(Unknown
> Source)
> > at org.semanticweb.HermiT.Reasoner.getTypes(Unknown Source)
> > at
> >
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:46)
> > at
> >
> org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator.addAxioms(InferredClassAssertionAxiomGenerator.java:42)
> > at
> >
> org.semanticweb.owlapi.util.InferredEntityAxiomGenerator.createAxioms(InferredEntityAxiomGenerator.java:49)
> > at
> >
> org.semanticweb.owlapi.util.InferredOntologyGenerator.fillOntology(InferredOntologyGenerator.java:111)
> > at
> > prototype.PrototypeFrame.InferredInstances(PrototypeFrame.java:898)
> > at
> >
> prototype.PrototypeFrame.BtnInferenceActionPerformed(PrototypeFrame.java:203)
> > at prototype.PrototypeFrame.access$200(PrototypeFrame.java:36)
> > at
> > prototype.PrototypeFrame$4.actionPerformed(PrototypeFrame.java:98)
> > at
> > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
> > at
> >
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
> > at
> >
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> > at
> > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> > at
> >
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> > at java.awt.Component.processMouseEvent(Component.java:6263)
> > at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> > at java.awt.Component.processEvent(Component.java:6028)
> > at java.awt.Container.processEvent(Container.java:2041)
> > at java.awt.Component.dispatchEventImpl(Component.java:4630)
> > at java.awt.Container.dispatchEventImpl(Container.java:2099)
> > at java.awt.Component.dispatchEvent(Component.java:4460)
> > at
> > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
> > at
> > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
> > at
> > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
> > at java.awt.Container.dispatchEventImpl(Container.java:2085)
> > at java.awt.Window.dispatchEventImpl(Window.java:2478)
> > at java.awt.Component.dispatchEvent(Component.java:4460)
> > at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
> > at
> >
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
> > at
> >
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
> > at
> >
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
> > at
> > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
> > at
> > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
> > at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
> >
> >
> -------------------------------------------------------------------------
> > You still did not send the stack trace for your exception. An example
> > of a stack trace for an exception would be something like this:
> >
> > java.lang.ClassCastException:
> > uk.ac.manchester.cs
> > .owl.owlapi.OWLObjectAllValuesFromImpl
> > cannot be cast
> > to org.semanticweb.owlapi.model.OWLClass
> > atuk.ac.manchester.cs
> >
> .owl.owlapi.OWLClassImpl.compareObjectOfSameType(OWLClassImpl.java:434)
> > at uk.ac.manchester.cs
> >
> .owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:167)
> > at
> > uk.ac.manchester.cs
> .owl.owlapi.OWLObjectImpl.compareTo(OWLObjectImpl.java:41)
> > at java.util.TreeMap.put(TreeMap.java:562)
> > at java.util.TreeSet.add(TreeSet.java:255)
> > at uk.ac.manchester.cs
> >
> .owl.owlapi.OWLClassImpl.getSuperClasses(OWLClassImpl.java:206)
> >
> >
> >
> > Each line in such a trace provides some additional information for a
> > developer to analyze.
> >
> > I would say that the API is working because I have modified some code in
> > Protege 4 recently that looks very much like what you are writing. The
> > code invoked by Protege 4.1 by File->Export Inferred Hierarchy is very
> > similar to yours.
> >
> > -Timothy
> >
> >
> > On 10/12/2010 09:28 AM, Soha Said wrote:
> > > Hello,
> > > I trace the error and I find the error in this line:
> > > InferredGenerator.add(new InferredClassAssertionAxiomGenerator());
> > > when I replced with this line:
> > > InferredGenerator.add(new InferredPropertyAssertionGenerator());
> > > it worked without error, but when I open the protege, the object
> > > properties are not saved correctly.
> > > for example, each individual will have its object properties and
> > > linked to the other individuals by TopObjectProperty like individual x
> > > and y, and x has TopObjectProperty is y and vise versa.
> > > when i classify from the protege interface, it inferred the properties
> > > correctly, but using api i think there is some problem.
> > >
> > > On 10/10/2010 07:06 AM, Soha Said wrote:
> > > > I used protege 4.1 beta build 209 api, and I have a problem in
> > > > inference api.
> > > > This is the snapshot of code that I used to get inferencing:
> > > > OWLOntologyManager
> > > ontologymanager=OWLManager.createOWLOntologyManager();
> > > > OWLOntology
> > > > ontology=ontologymanager.loadOntology(IRI.create(OwlUri));
> > > > OWLDataFactory
> factory=ontologymanager.getOWLDataFactory();
> > > > OWLReasonerFactory reasonerfactory= new
> > > > Reasoner.ReasonerFactory();
> > > > OWLReasoner
> > > > owlreasoner=reasonerfactory.createNonBufferingReasoner(ontology);
> > > >
> > > > owlreasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
> > > >
> > > > List> InferredGenerator =
> > > > new ArrayList>();
> > > > InferredGenerator.add(new
> > > > InferredClassAssertionAxiomGenerator());
> > > > InferredOntologyGenerator ontologygenerator=new
> > > > InferredOntologyGenerator(owlreasoner,InferredGenerator);
> > > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > >
> ontologymanager.saveOntology(ontology,IRI.create(OwlUri));
> > > > but I have an exception in this line:
> > > > ontologygenerator.fillOntology(ontologymanager,ontology);
> > > > this exception says: java.lang.NullPointerException
> > > > I don't know what i should do and what is wrong.
> > > > Thanks in advance
> > > > Soha Said
> > > >
> >
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From rucha_kale06 at yahoo.com Mon Oct 18 10:29:06 2010
From: rucha_kale06 at yahoo.com (rucha kale)
Date: Mon, 18 Oct 2010 10:29:06 -0700 (PDT)
Subject: [protege-discussion] (no subject)
Message-ID: <900324.97670.qm@web55207.mail.re4.yahoo.com>
http://projekt-fokus.de/sinfo.php
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From binary.nurse at gmail.com Tue Oct 19 04:04:28 2010
From: binary.nurse at gmail.com (Phil Shields)
Date: Tue, 19 Oct 2010 22:04:28 +1100
Subject: [protege-discussion] dumb questions
Message-ID:
Hi, I am learning about protege but I don't understand where object
properties are identified as being attached to their individual(s) If
I click onto an object property should the editor display the linked
entities?
I am mapping documentation used in our ward and would like to identify
data properties as being grouped into one of four domains can I do
this?
Sorry if this is blatantly obvious but I'm new to it all. Cheers Phil.
--
? ? ? ? ? ? ? ? ?? :? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? :? ? |
`?.??.??>`?.??.???`?.?.???`?...?>? J
From h.alani at open.ac.uk Tue Oct 19 05:21:19 2010
From: h.alani at open.ac.uk (Harith Alani)
Date: Tue, 19 Oct 2010 13:21:19 +0100
Subject: [protege-discussion] Fwd: Fwd: Full time PhD in Social Semantics -
KMi, OU, UK
Message-ID: <4CBD8D3F.7000008@open.ac.uk>
[apologies for cross-posting]
http://kmi.open.ac.uk/studentships/social-semantics.php
*Full-time PhD studentship in Social Semantics*
Knowledge Media Institute
Based in Milton Keynes
Three-year PhD studentship
*Application deadline: 8 November 2010*
The PhD studentship will provide a tax-free stipend of ?13,590
(increases on an annual basis) and covers all fees, and is available to
any suitably qualified UK, EU and International student.
Start Date: January 2011 (or later by agreement).
The explosive growth of online communities continues in all areas of
society, and their use is now widespread in social, business, scientific
and public service domains, enabling community members to collaborate
through shared ideas, knowledge and opinion. Online communities now
generate major economic value to business and can form pivotal parts of
corporate expertise management, corporate marketing, product support,
customer relationship management, product innovation and targeted
advertising.
However, the micro and macro dynamics of online communities in terms of
structure, information, behaviour and economics are not well understood.
There is a real need for far better real-time tracking of individuals,
sub-communities, interests, and behaviours, all supported by in-depth
analytics and a framework for automated, speedy generation of rich user
profiles.
This PhD project will focus on designing and developing tools to monitor
and process users? activities in online communities to identify and
evaluate their interests and behaviour over time, using a combination of
syntactical, statistical, and semantic analysis techniques. Semantic
technologies will be used to model, structure, integrate, and process
user profiles.
This studentship is funded by both the Open University and an EU project
that involves several academic and industrial partners from various
European countries. The aim of this project is to design and develop a
platform for real-time monitoring and analysis of business online
communities.
Academic Requirements: You should have a first or upper second-class
honours undergraduate degree or a relevant Masters Degree or equivalent
experience in a relevant computer science discipline. Knowledge of
semantic web technologies is a clear advantage.
How to Apply: Be sure to refer to the online prospectus at
http://www3.open.ac.uk/study/research-degrees/computing.htm and download
and complete the 10-page MPhil/PhD application form. Applications should
be sent by email to Miss Ortenz Rose, including a covering letter, a
research proposal (a maximum of 2,000 words) and a full CV, giving
contact details for two academic referees.
Application deadline: 8 November 2010
Interviews: week commencing 22 November 2010
--
The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302).
From h.alani at open.ac.uk Tue Oct 19 05:21:46 2010
From: h.alani at open.ac.uk (Harith Alani)
Date: Tue, 19 Oct 2010 13:21:46 +0100
Subject: [protege-discussion] Full time PhD in Topic/Sentiment Tracking and
Analysis - KMi, OU, UK
Message-ID: <4CBD8D5A.8060406@open.ac.uk>
[apologies for cross-posting]
http://kmi.open.ac.uk/studentships/topic-sentiment-tracking-and-analysis.php
*Full-time PhD studentship in Topic/Sentiment Tracking and Analysis*
Knowledge Media Institute
Based in Milton Keynes
Three-year PhD studentship
*Application deadline: 8 November 2010*
The PhD studentship will provide a tax-free stipend of ?13,590
(increases on an annual basis) and covers all fees, and is available to
any suitably qualified UK, EU and International student.
Start Date: January 2011 (or later by agreement).
Background: With the explosion of people's attitudes and opinions
expressed in social media including blogs, discussion forums, tweets,
etc, detecting sentiment or opinion from the Web is becoming an
increasingly popular way of interpreting data. Sentiment analysis is
concerned with automatically identifying sentiment or opinion expressed
in a given piece of text. It finds wide applications in tracking
companies' reputations, finding customers' opinions about
products/services and competitors, monitoring positive or negative
trends in social media, etc.
This studentship is funded by both the Open University and an EU project
that involves several academic and industrial partners from various
European countries. The aim of this project is to design and develop a
platform for real-time monitoring and analysis of business online
communities.
Project: This PhD project aims to use semantic technologies to develop
novel techniques for topic/sentiment extraction and monitoring from
blogs, forums, and other social media using techniques from machine
learning, natural language processing, information retrieval, data
mining, and semantic web. In particular, it will focus on detecting,
tracking and qualitatively measuring topic ebb and flow, providing views
of current and recurrent interests and shifts in topic and sentiment.
This project will also identify community roles such as topic
innovators, summarisers, answer-givers or the content of topics likely
to engender disputes.
Academic Requirements: You should have a first or upper second-class
honours undergraduate degree or a relevant Masters Degree or equivalent
experience in a relevant computer science discipline. Knowledge of
natural language processing or machine learning would be desirable.
How to Apply: Be sure to refer to the online prospectus at
http://www3.open.ac.uk/study/research-degrees/computing.htm and download
and complete the 10-page MPhil/PhD application form. Applications should
be sent by email to Miss Ortenz Rose, including a covering letter, a
research proposal (a maximum of 2,000 words) and a full CV, giving
contact details for two academic referees.
Application deadline: 8 November 2010
Interviews: week commencing 22 November 2010
--
The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302).
From tredmond at stanford.edu Tue Oct 19 13:06:52 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 19 Oct 2010 13:06:52 -0700
Subject: [protege-discussion] questions
In-Reply-To:
References:
Message-ID: <4CBDFA5C.20005@stanford.edu>
On 10/19/2010 04:04 AM, Phil Shields wrote:
> Hi, I am learning about protege but I don't understand where object
> properties are identified as being attached to their individual(s) If
> I click onto an object property should the editor display the linked
> entities?
>
This can be seen in the individuals tab. Click on an individual and you
will see the property values for that individual on the right.
> I am mapping documentation used in our ward and would like to identify
> data properties as being grouped into one of four domains can I do
> this?
>
>
What do you mean by this exactly? The first thing that occurs to me is
that you are saying that these four data properties can only be applied
to four different disjoint classes. That can be said by setting the
domains of the data properties (which can be done in the properties
tab). This could be done with an ontology something like the following:
DataProperty: p
Domain:
A
DataProperty: q
Domain:
B
DataProperty: r
Domain:
C
DataProperty: s
Domain:
D
Class: A
Class: D
Class: C
Class: B
DisjointClasses:
A,B,C,D
-Timothy
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From binary.nurse at gmail.com Tue Oct 19 15:27:55 2010
From: binary.nurse at gmail.com (Phil Shields)
Date: Wed, 20 Oct 2010 09:27:55 +1100
Subject: [protege-discussion] questions
In-Reply-To: <4CBDFA5C.20005@stanford.edu>
References:
<4CBDFA5C.20005@stanford.edu>
Message-ID:
On Wed, Oct 20, 2010 at 7:06 AM, Timothy Redmond wrote:
> On 10/19/2010 04:04 AM, Phil Shields wrote:
>
> Hi, I am learning about protege but I don't understand where object
> properties are identified as being attached to their individual(s) If
> I click onto an object property should the editor display the linked
> entities?
>
>
> This can be seen in the individuals tab.? Click on an individual and you
> will see the property values for that individual on the right.
Thanks! I knew it would be simple...at this stage I just couldn't see it.
>
> I am mapping documentation used in our ward and would like to identify
> data properties as being grouped into one of four domains can I do
> this?
>
>
>
> What do you mean by this exactly? The first thing that occurs to me is that
> you are saying that these four data properties can only be applied to four
> different disjoint classes.? That can be said by setting the domains of the
> data properties (which can be done in the properties tab).? This could be
> done with an ontology something like the following:
>
> DataProperty: p
> Domain:
> A
>
> DataProperty: q
> Domain:
> B
>
> DataProperty: r
> Domain:
> C
>
> DataProperty: s
> Domain:
> D
>
> Class: A
> Class: D
> Class: C
> Class: B
>
> DisjointClasses:
> A,B,C,D
>
>
> -Timothy
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
Thanks for that Timothy, in a typical Medical ward the clinical
documentation has many data redundancies. Nursing has three major
theoretical domains
and they are:
Physical,Social, psychological and spiritual.
The physical documentation is grouped together in a heirachy of:
Patient identification, allergy information and event date time stamp
Admission documentation Clinical documentation Discharge documentation
This heirachy works very well.
Each document in the above classes have data properties such as an
blood pressure in the observation document in clinical documentation,
this would fall under the "physical" domain.
In one document most data properties fall under the physical domain
some in the social and some in the psychological. I would like to
identify what "domains" the data properties fall in to. Also I would
like to have slots between data properties in different documents
identifying their similarity to other data properties in other
documents.
This is fun and I may even map out the catastrophe that is clinical
documentation...this is a high ideal I know, but I just do one little
thing at a time..Thanks for your help,
De Phil Shields (ward nurse).
--
? ? ? ? ? ? ? ? ?? :? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? :? ? |
`?.??.??>`?.??.???`?.?.???`?...?>? J
From linikujp at yahoo.co.jp Wed Oct 20 16:31:13 2010
From: linikujp at yahoo.co.jp (Yu Lin)
Date: Thu, 21 Oct 2010 08:31:13 +0900 (JST)
Subject: [protege-discussion] How to check the inconsistence
Message-ID: <20101020233113.77271.qmail@web4108.mail.ogk.yahoo.co.jp>
Hi, Dear all,
I am using protege 4.1 version, and HermiT reasoner 1.3.1
The program shows the following inconsistence log:
Error 221 Logged at Thu Oct 21 08:14:13 JST 2010
InconsistentOntologyException: Inconsistent ontology
org.semanticweb.HermiT.Reasoner.throwInconsistentOntologyExceptionIfNecessary(Unknown
Source)
org.semanticweb.HermiT.Reasoner.checkPreConditions(Unknown
Source)
org.semanticweb.HermiT.Reasoner.isSatisfiable(Unknown
Source)
org.protege.editor.owl.ui.renderer.OWLCellRenderer$1.run(OWLCellRenderer.java:766)
org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask
(ReasonerPreferences.java:181)
org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken
(OWLCellRenderer.java:763)
org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightText
(OWLCellRenderer.java:721)
org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane
(OWLCellRenderer.java:698)
org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer
(OWLCellRenderer.java:469)
org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent
(OWLCellRenderer.java:361)
org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent
(OWLObjectTreeCellRenderer.java:34)
javax.swing.plaf.basic.BasicTreeUI.paintRow(Unknown
Source)
javax.swing.plaf.basic.BasicTreeUI.paint(Unknown
Source)
javax.swing.plaf.ComponentUI.update(Unknown Source)
javax.swing.JComponent.paintComponent(Unknown Source)
org.protege.editor.owl.ui.tree.OWLObjectTree.paintComponent(OWLObjectTree.java:666)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JViewport.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JSplitPane.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JSplitPane.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JLayeredPane.paint(Unknown Source)
javax.swing.JComponent.paintChildren(Unknown Source)
javax.swing.JComponent.paint(Unknown Source)
javax.swing.JComponent.paintWithOffscreenBuffer(Unknown
Source)
javax.swing.JComponent.paintDoubleBuffered(Unknown
Source)
javax.swing.JComponent._paintImmediately(Unknown
Source)
javax.swing.JComponent.paintImmediately(Unknown
Source)
javax.swing.RepaintManager.paintDirtyRegions(Unknown
Source)
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
Source)
java.awt.event.InvocationEvent.dispatch(Unknown
Source)
java.awt.EventQueue.dispatchEvent(Unknown Source)
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown
Source)
java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
Source)
java.awt.EventDispatchThread.pumpEvents(Unknown
Source)
java.awt.EventDispatchThread.pumpEvents(Unknown
Source)
java.awt.EventDispatchThread.run(Unknown Source)
------------------------------------------------------------------------------------------
---------
I had no idea of what are these codes talking about.
Could anyone please tell me how to find a clue for solving
the problem?
The previous version of protege can give intructions on
which terms or porperties are inconsistent with each
other. Unfortunately, in Protege 4 this function has been
deleted. :(
Thank you very much.
Yours sincerely,
Aisyah Yu Lin
From tredmond at stanford.edu Wed Oct 20 17:47:20 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Wed, 20 Oct 2010 17:47:20 -0700
Subject: [protege-discussion] How to check the inconsistence
In-Reply-To: <20101020233113.77271.qmail@web4108.mail.ogk.yahoo.co.jp>
References: <20101020233113.77271.qmail@web4108.mail.ogk.yahoo.co.jp>
Message-ID: <4CBF8D98.8040900@stanford.edu>
> I had no idea of what are these codes talking about.
> Could anyone please tell me how to find a clue for solving
> the problem?
>
>
Unfortunately I don't know how to handle this case yet. The problem is
that a reasoner will refuse to function with an inconsistent ontology.
Inconsistent classes or properties are fine but when the whole ontology
is inconsistent the reasoner is stuck. Unfortunately the best solution
that I know for this at present is to use a command line tool. Download
pellet (http://clarkparsia.com/pellet/) and run
pellet.sh explain --inconsistent ...your ontology...
> The previous version of protege can give intructions on
> which terms or porperties are inconsistent with each
> other. Unfortunately, in Protege 4 this function has been
> deleted. :(
This has actually been revived with the latest Protege 4.1 and the
latest updates. We should have a release with this functionality soon.
But unfortunately this will still not cover your case.
-Timothy
On 10/20/2010 04:31 PM, Yu Lin wrote:
> Hi, Dear all,
>
> I am using protege 4.1 version, and HermiT reasoner 1.3.1
>
> The program shows the following inconsistence log:
>
> Error 221 Logged at Thu Oct 21 08:14:13 JST 2010
> InconsistentOntologyException: Inconsistent ontology
>
> org.semanticweb.HermiT.Reasoner.throwInconsistentOntologyExceptionIfNecessary(Unknown
>
>
> Source)
>
> org.semanticweb.HermiT.Reasoner.checkPreConditions(Unknown
> Source)
> org.semanticweb.HermiT.Reasoner.isSatisfiable(Unknown
> Source)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer$1.run(OWLCellRenderer.java:766)
>
> org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask
>
> (ReasonerPreferences.java:181)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken
>
> (OWLCellRenderer.java:763)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightText
>
> (OWLCellRenderer.java:721)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane
>
> (OWLCellRenderer.java:698)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer
>
> (OWLCellRenderer.java:469)
>
> org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent
>
> (OWLCellRenderer.java:361)
>
> org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent
>
> (OWLObjectTreeCellRenderer.java:34)
> javax.swing.plaf.basic.BasicTreeUI.paintRow(Unknown
> Source)
> javax.swing.plaf.basic.BasicTreeUI.paint(Unknown
> Source)
> javax.swing.plaf.ComponentUI.update(Unknown Source)
> javax.swing.JComponent.paintComponent(Unknown Source)
>
> org.protege.editor.owl.ui.tree.OWLObjectTree.paintComponent(OWLObjectTree.java:666)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JViewport.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JSplitPane.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JSplitPane.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
> javax.swing.JLayeredPane.paint(Unknown Source)
> javax.swing.JComponent.paintChildren(Unknown Source)
> javax.swing.JComponent.paint(Unknown Source)
>
> javax.swing.JComponent.paintWithOffscreenBuffer(Unknown
> Source)
> javax.swing.JComponent.paintDoubleBuffered(Unknown
> Source)
> javax.swing.JComponent._paintImmediately(Unknown
> Source)
> javax.swing.JComponent.paintImmediately(Unknown
> Source)
> javax.swing.RepaintManager.paintDirtyRegions(Unknown
> Source)
>
> javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
> Source)
> java.awt.event.InvocationEvent.dispatch(Unknown
> Source)
> java.awt.EventQueue.dispatchEvent(Unknown Source)
>
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown
> Source)
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
> Source)
> java.awt.EventDispatchThread.pumpEvents(Unknown
> Source)
> java.awt.EventDispatchThread.pumpEvents(Unknown
> Source)
> java.awt.EventDispatchThread.run(Unknown Source)
> ------------------------------------------------------------------------------------------
>
> ---------
>
> I had no idea of what are these codes talking about.
> Could anyone please tell me how to find a clue for solving
> the problem?
>
> The previous version of protege can give intructions on
> which terms or porperties are inconsistent with each
> other. Unfortunately, in Protege 4 this function has been
> deleted. :(
>
>
> Thank you very much.
>
> Yours sincerely,
> Aisyah Yu Lin
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
-------------- next part --------------
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From linikujp at yahoo.co.jp Thu Oct 21 05:12:50 2010
From: linikujp at yahoo.co.jp (Yu Lin)
Date: Thu, 21 Oct 2010 21:12:50 +0900 (JST)
Subject: [protege-discussion] How to check the inconsistence
In-Reply-To: <4CBF8D98.8040900@stanford.edu>
Message-ID: <20101021121250.4001.qmail@web4107.mail.ogk.yahoo.co.jp>
Thank you,
I will try the tool.
Asiyah
--- Timothy Redmond wrote:
>
> > I had no idea of what are these codes talking
> about.
> > Could anyone please tell me how to find a clue for
> solving
> > the problem?
> >
> >
>
> Unfortunately I don't know how to handle this case
> yet. The problem is
> that a reasoner will refuse to function with an
> inconsistent ontology.
> Inconsistent classes or properties are fine but when
> the whole ontology
> is inconsistent the reasoner is stuck.
> Unfortunately the best solution
> that I know for this at present is to use a command
> line tool. Download
> pellet (http://clarkparsia.com/pellet/) and run
>
> pellet.sh explain --inconsistent ...your
> ontology...
>
>
> > The previous version of protege can give
> intructions on
> > which terms or porperties are inconsistent with
> each
> > other. Unfortunately, in Protege 4 this function
> has been
> > deleted. :(
>
> This has actually been revived with the latest
> Protege 4.1 and the
> latest updates. We should have a release with this
> functionality soon.
> But unfortunately this will still not cover your
> case.
>
> -Timothy
>
>
> On 10/20/2010 04:31 PM, Yu Lin wrote:
> > Hi, Dear all,
> >
> > I am using protege 4.1 version, and HermiT
> reasoner 1.3.1
> >
> > The program shows the following inconsistence log:
> >
> > Error 221 Logged at Thu Oct 21 08:14:13 JST 2010
> > InconsistentOntologyException: Inconsistent
> ontology
> >
> >
>
org.semanticweb.HermiT.Reasoner.throwInconsistentOntologyExceptionIfNecessary(Unknown
> >
> >
> > Source)
> >
> >
>
org.semanticweb.HermiT.Reasoner.checkPreConditions(Unknown
> > Source)
> >
> org.semanticweb.HermiT.Reasoner.isSatisfiable(Unknown
> > Source)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer$1.run(OWLCellRenderer.java:766)
> >
> >
>
org.protege.editor.owl.model.inference.ReasonerPreferences.executeTask
> >
> > (ReasonerPreferences.java:181)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer.renderToken
> >
> > (OWLCellRenderer.java:763)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer.highlightText
> >
> > (OWLCellRenderer.java:721)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareTextPane
> >
> > (OWLCellRenderer.java:698)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer.prepareRenderer
> >
> > (OWLCellRenderer.java:469)
> >
> >
>
org.protege.editor.owl.ui.renderer.OWLCellRenderer.getTreeCellRendererComponent
> >
> > (OWLCellRenderer.java:361)
> >
> >
>
org.protege.editor.owl.ui.tree.OWLObjectTreeCellRenderer.getTreeCellRendererComponent
> >
> > (OWLObjectTreeCellRenderer.java:34)
> >
> javax.swing.plaf.basic.BasicTreeUI.paintRow(Unknown
> > Source)
> >
> javax.swing.plaf.basic.BasicTreeUI.paint(Unknown
> > Source)
> > javax.swing.plaf.ComponentUI.update(Unknown
> Source)
> > javax.swing.JComponent.paintComponent(Unknown
> Source)
> >
> >
>
org.protege.editor.owl.ui.tree.OWLObjectTree.paintComponent(OWLObjectTree.java:666)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JViewport.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JSplitPane.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JSplitPane.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> > javax.swing.JLayeredPane.paint(Unknown
> Source)
> > javax.swing.JComponent.paintChildren(Unknown
> Source)
> > javax.swing.JComponent.paint(Unknown Source)
> >
> >
> javax.swing.JComponent.paintWithOffscreenBuffer(Unknown
> > Source)
> >
> javax.swing.JComponent.paintDoubleBuffered(Unknown
> > Source)
> >
> javax.swing.JComponent._paintImmediately(Unknown
> > Source)
> >
> javax.swing.JComponent.paintImmediately(Unknown
> > Source)
> >
> javax.swing.RepaintManager.paintDirtyRegions(Unknown
> > Source)
> >
> >
>
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown
> > Source)
> >
> java.awt.event.InvocationEvent.dispatch(Unknown
>
=== ???????????????? ===>
_______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
>
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
From vjoh at inform.com Thu Oct 21 07:26:00 2010
From: vjoh at inform.com (Veronica Joh)
Date: Thu, 21 Oct 2010 10:26:00 -0400
Subject: [protege-discussion] rdf visualization in protege?
Message-ID:
Hi
I'm pretty new to protege, and I am trying to view rdf xml in Protege.
Is it possible to load my rdf/xml in Protege and view the data inside it?
I tried to load rdf/xml in Protege but I keep getting error saying the file
is not well-formed.
If this is not possible, can you please recommend any other tools that
allows you to view data in RDF file, besides loading it to sesame?
Thank you!
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From rcaschultz at gmail.com Sun Oct 24 19:28:33 2010
From: rcaschultz at gmail.com (Ron Schultz)
Date: Sun, 24 Oct 2010 21:28:33 -0500
Subject: [protege-discussion] Programmatically override the maximum
cardinality for a slot, varying it by Cls
Message-ID:
I have a circumstance where different Clses contain the slot 'keyword.' The
keyword slot is of valueType 'String,' with a default maximum cardinality
set to 1.
I have a requirement to vary this cardinality class by class. I am just not
sure how to do this programmatically.
Let's say I have a class 'Article' where I want to set the maximum number of
keywords to 5.
Do I:
- Get the slot 'keywords' from the cls 'Article', and then set the values
of keyword's slot named :SLOT-MAXIMUM-CARDINALITY to a Collection containing
5?
- Or do I perform some operations using the facets of the slot 'keyword.'
- Or ...?
I've spent all weekend trying to figure this out and I know I must be
missing something obvious.
Thanks.
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From h.alani at open.ac.uk Mon Oct 25 01:19:30 2010
From: h.alani at open.ac.uk (Harith Alani)
Date: Mon, 25 Oct 2010 09:19:30 +0100
Subject: [protege-discussion] Call for Papers for ESWC 2010 Sensor Web Track
Message-ID: <4CC53D92.7040805@open.ac.uk>
[apologies for cross-posting!]
---------------------------------------------------------------------
CALL FOR PAPERS
---------------------------------------------------------------------
The 8th Extended Semantic Web Conference (ESWC),
*Sensor Web Track*
http://www.eswc2011.org/
May 29 - June 2, 2011, Heraklion, Greece
* Abstract submission: December 6, 2010 (compulsory) *
* Full-paper submission: December 13, 2010 (11:59 pm Hawaii time) *
*Sensor Web Track*
http://www.eswc2011.org/content/cfp#Sensor%20Web
The correct interpretation and analysis of the raw numerical values
provided by the ever more pervasive sensor networks requires proper
semantics support and contextual knowledge. This enables better data
representation, integration, and use, and further aids in coping with
the inherently unreliable nature of the observations provided by sensor
networks, affected by sensor noise and faults. In this track we invite
approaches dealing with combining sensor network and semantic
technologies, for the purpose of management, interpretation and analysis
of the observed environment. Contributions are expected to cover a wide
range of related topics such as (a)identification of simple events or
event streams by joining sensor data with background knowledge, (b)
identification of complex events composed from several atomic sensed
events based on background knowledge, (c) filtering, management, and
interpretation of sensor data using contextual models, (d) creation of
actuators and applications based on sensor data and background
knowledge. We also particularly welcome solutions that address one or
more of the above challenges by means of in-network processing techniques.
*Topics of Interest*
We invite high-quality submissions related to (but not limited to) one
or more of the following topics:
- Data models and querying solutions for semantic sensor networks
- Programming languages and abstractions for sensor network supporting
contextual and background models
- Architectures and middleware for semantic sensor networks
- In-network data processing and filtering techniques based on
contextual and semantic knowledge
- Ontologies and rules for semantic sensor networks
- Annotation tools for semantic sensor networks
- Semantic data integration and fusion of heterogeneous sensor network
data streams
- Spatio-temporal aspects of semantic sensor networks
- Filtering techniques for sensor network data based on contextual knowledge
- Mash-up technologies for semantic sensor networks
- Use cases and applications demonstrating the use of semantic
technologies combined with sensor networks
- Social sensing data architectures and applications
- Standardization efforts in semantic sensor networks
- Visualisation of semantic sensor data
*Submission Details*
The proceedings of the conference will be published in Springer's
Lecture Notes in Computer Science series. Papers must not exceed fifteen
(15) pages in length and must be formatted according to the information
for LNCS authors. At least one author of each accepted paper must
register for the conference in order for the paper to be included in the
conference proceedings. Papers for the Sensor Web track should be
submitted at:
http://www.easychair.org/conferences/?conf=eswc2011sensors
*Important Dates*
* Abstract submission: December 6, 2010 (compulsory)
* Full-paper submission: December 13, 2010 (11:59 pm Hawaii time)
* Notification of acceptance/rejection: February 21, 2011
* Camera-ready papers: March 7, 2011
*Chairs*
Harith Alani - Knowledge Media Institute, OU, UK
Luca Mottola - Swedish Insitute of Computer Science, SE
--
The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302).
From h.alani at open.ac.uk Mon Oct 25 01:24:11 2010
From: h.alani at open.ac.uk (Harith Alani)
Date: Mon, 25 Oct 2010 09:24:11 +0100
Subject: [protege-discussion] Call for Papers for *ESWC 2011* Sensor Web
Track
In-Reply-To: <4CC53D92.7040805@open.ac.uk>
References: <4CC53D92.7040805@open.ac.uk>
Message-ID: <4CC53EAB.4020307@open.ac.uk>
On 25/10/2010 09:19, Harith Alani wrote:
> [apologies for cross-posting!]
> ---------------------------------------------------------------------
> CALL FOR PAPERS
> ---------------------------------------------------------------------
>
>
> The 8th Extended Semantic Web Conference (ESWC),
> *Sensor Web Track*
> http://www.eswc2011.org/
> May 29 - June 2, 2011, Heraklion, Greece
>
>
> * Abstract submission: December 6, 2010 (compulsory) *
> * Full-paper submission: December 13, 2010 (11:59 pm Hawaii time) *
>
>
> *Sensor Web Track*
>
> http://www.eswc2011.org/content/cfp#Sensor%20Web
>
> The correct interpretation and analysis of the raw numerical values
> provided by the ever more pervasive sensor networks requires proper
> semantics support and contextual knowledge. This enables better data
> representation, integration, and use, and further aids in coping with
> the inherently unreliable nature of the observations provided by sensor
> networks, affected by sensor noise and faults. In this track we invite
> approaches dealing with combining sensor network and semantic
> technologies, for the purpose of management, interpretation and analysis
> of the observed environment. Contributions are expected to cover a wide
> range of related topics such as (a)identification of simple events or
> event streams by joining sensor data with background knowledge, (b)
> identification of complex events composed from several atomic sensed
> events based on background knowledge, (c) filtering, management, and
> interpretation of sensor data using contextual models, (d) creation of
> actuators and applications based on sensor data and background
> knowledge. We also particularly welcome solutions that address one or
> more of the above challenges by means of in-network processing techniques.
>
> *Topics of Interest*
>
> We invite high-quality submissions related to (but not limited to) one
> or more of the following topics:
> - Data models and querying solutions for semantic sensor networks
> - Programming languages and abstractions for sensor network supporting
> contextual and background models
> - Architectures and middleware for semantic sensor networks
> - In-network data processing and filtering techniques based on
> contextual and semantic knowledge
> - Ontologies and rules for semantic sensor networks
> - Annotation tools for semantic sensor networks
> - Semantic data integration and fusion of heterogeneous sensor network
> data streams
> - Spatio-temporal aspects of semantic sensor networks
> - Filtering techniques for sensor network data based on contextual knowledge
> - Mash-up technologies for semantic sensor networks
> - Use cases and applications demonstrating the use of semantic
> technologies combined with sensor networks
> - Social sensing data architectures and applications
> - Standardization efforts in semantic sensor networks
> - Visualisation of semantic sensor data
>
> *Submission Details*
>
> The proceedings of the conference will be published in Springer's
> Lecture Notes in Computer Science series. Papers must not exceed fifteen
> (15) pages in length and must be formatted according to the information
> for LNCS authors. At least one author of each accepted paper must
> register for the conference in order for the paper to be included in the
> conference proceedings. Papers for the Sensor Web track should be
> submitted at:
>
> http://www.easychair.org/conferences/?conf=eswc2011sensors
>
> *Important Dates*
>
> * Abstract submission: December 6, 2010 (compulsory)
> * Full-paper submission: December 13, 2010 (11:59 pm Hawaii time)
> * Notification of acceptance/rejection: February 21, 2011
> * Camera-ready papers: March 7, 2011
>
>
> *Chairs*
> Harith Alani - Knowledge Media Institute, OU, UK
> Luca Mottola - Swedish Insitute of Computer Science, SE
>
>
>
--
The Open University is incorporated by Royal Charter (RC 000391), an exempt charity in England & Wales and a charity registered in Scotland (SC 038302).
From umut0815 at yahoo.com Mon Oct 25 11:06:12 2010
From: umut0815 at yahoo.com (Umut)
Date: Mon, 25 Oct 2010 11:06:12 -0700 (PDT)
Subject: [protege-discussion] Heap space and runtime problem
Message-ID: <513533.91328.qm@web52503.mail.re2.yahoo.com>
Dear all!
Im new to the Protege API and im currently trying to develope an ontology for
Sensor Observation Services.
Theses services can contain several hundred sensors, and this is where the
trouble starts. When I map the Sensor Observation Service into my OWL ontology I
have to create individuals of all sensors and their attributes (~20 per Sensor).
Especially the creating of properties between all the attributes and the sensors
takes a lot of time (30-40min, which is actually not a big problem) and
apparently heap space.
No matter how much I increase the heap space my program crashes when mapping
Sensor Observation Services with more than 300 Sensors.
Is this normal or do I have some unefficient code? If yes, any ideas where I
should check?
Im also open for different solutions to solve the problem :D
Thanks a lot!
Umut
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From tar at isi.edu Mon Oct 25 11:09:26 2010
From: tar at isi.edu (Thomas Russ)
Date: Mon, 25 Oct 2010 11:09:26 -0700
Subject: [protege-discussion] Programmatically override the maximum
cardinality for a slot, varying it by Cls
In-Reply-To:
References:
Message-ID: <3BCB04D6-389C-4AD2-A340-46B650C1301B@isi.edu>
On Oct 24, 2010, at 7:28 PM, Ron Schultz wrote:
> I have a circumstance where different Clses contain the slot
> 'keyword.' The keyword slot is of valueType 'String,' with a default
> maximum cardinality set to 1.
>
> I have a requirement to vary this cardinality class by class. I am
> just not sure how to do this programmatically.
>
> Let's say I have a class 'Article' where I want to set the maximum
> number of keywords to 5.
>
> Do I:
> ? Get the slot 'keywords' from the cls 'Article', and then set the
> values of keyword's slot named :SLOT-MAXIMUM-CARDINALITY to a
> Collection containing 5?
> ? Or do I perform some operations using the facets of the slot
> 'keyword.'
> ? Or ...?
> I've spent all weekend trying to figure this out and I know I must
> be missing something obvious.
Not completely sure about this, but it looks like this may be what you
are looking for:
http://protege.stanford.edu/doc/pdk/working_with_facets.html
From tar at isi.edu Mon Oct 25 11:12:45 2010
From: tar at isi.edu (Thomas Russ)
Date: Mon, 25 Oct 2010 11:12:45 -0700
Subject: [protege-discussion] Heap space and runtime problem
In-Reply-To: <513533.91328.qm@web52503.mail.re2.yahoo.com>
References: <513533.91328.qm@web52503.mail.re2.yahoo.com>
Message-ID: <93DA7354-F471-4F75-866E-3FFAB82DECAC@isi.edu>
On Oct 25, 2010, at 11:06 AM, Umut wrote:
> Dear all!
>
> Im new to the Protege API and im currently trying to develope an
> ontology for Sensor Observation Services.
> Theses services can contain several hundred sensors, and this is
> where the trouble starts. When I map the Sensor Observation Service
> into my OWL ontology I have to create individuals of all sensors and
> their attributes (~20 per Sensor). Especially the creating of
> properties between all the attributes and the sensors takes a lot of
> time (30-40min, which is actually not a big problem) and apparently
> heap space.
> No matter how much I increase the heap space my program crashes when
> mapping Sensor Observation Services with more than 300 Sensors.
> Is this normal or do I have some unefficient code? If yes, any ideas
> where I should check?
> Im also open for different solutions to solve the problem :D
This sounds like you would have about 6000 instances, which is a
reasonable, although not too huge size.
Which API are you using? Protege-OWL-API (Protege 3.x) or OWL-API
(Protege 4.x)?
Could you show us a bit of the code that you are running to create the
individuals, attributes and link them using properties?
From umut0815 at yahoo.com Mon Oct 25 11:38:47 2010
From: umut0815 at yahoo.com (Umut)
Date: Mon, 25 Oct 2010 11:38:47 -0700 (PDT)
Subject: [protege-discussion] Heap space and runtime problem
In-Reply-To: <93DA7354-F471-4F75-866E-3FFAB82DECAC@isi.edu>
References: <513533.91328.qm@web52503.mail.re2.yahoo.com>
<93DA7354-F471-4F75-866E-3FFAB82DECAC@isi.edu>
Message-ID: <880749.54496.qm@web52506.mail.re2.yahoo.com>
Hey!
Im using Protege 3.x API (also im not quite sure why ;)).
Actually it should be less than 6000 instances, because many of the sensors have
the same attributes. So one instance is linked to more than 1 sensor.
here is a bit of the code:
This is one method to add "observedProperties" to one sensor, all the other
methods are about the same.
private OWLNamedClass observedProperties;
private OWLObjectProperty hasObservedProperty;
....
observedProperties = owlModel.getOWLNamedClass("om-r:ObservedProperty");
hasObservedProperty = owlModel.getOWLObjectProperty("sos:hasObservedProperty");
....
public void addObservedProperty(Sensor sensor){
ArrayList observedProps = new ArrayList();
for(int j = 0; j < sensor.getObservedProperties().size();j++){
observedPropertyIndividual = (OWLIndividual)
owlModel.getSimpleInstance(sensor.getObservedProperties().get(j));
if(observedPropertyIndividual == null){
observedProps.add(observedProperties.createOWLIndividual(sensor.getObservedProperties().get(j)));
}else{
observedProps.add(observedPropertyIndividual);
}
}
sensorIndividual.setPropertyValues(hasObservedProperty, observedProps);
}
--------------------------------
If this is not what you need i?ll be happy to post more code :)
Thanks
bye
umut
________________________________
From: Thomas Russ
To: User support for Core Protege and the Protege-Frames editor
Sent: Mon, October 25, 2010 8:12:45 PM
Subject: Re: [protege-discussion] Heap space and runtime problem
On Oct 25, 2010, at 11:06 AM, Umut wrote:
> Dear all!
>
> Im new to the Protege API and im currently trying to develope an ontology for
>Sensor Observation Services.
> Theses services can contain several hundred sensors, and this is where the
>trouble starts. When I map the Sensor Observation Service into my OWL ontology I
>have to create individuals of all sensors and their attributes (~20 per Sensor).
>Especially the creating of properties between all the attributes and the sensors
>takes a lot of time (30-40min, which is actually not a big problem) and
>apparently heap space.
> No matter how much I increase the heap space my program crashes when mapping
>Sensor Observation Services with more than 300 Sensors.
> Is this normal or do I have some unefficient code? If yes, any ideas where I
>should check?
> Im also open for different solutions to solve the problem :D
This sounds like you would have about 6000 instances, which is a reasonable,
although not too huge size.
Which API are you using? Protege-OWL-API (Protege 3.x) or OWL-API (Protege
4.x)?
Could you show us a bit of the code that you are running to create the
individuals, attributes and link them using properties?
_______________________________________________
protege-discussion mailing list
protege-discussion at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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From sohaelshafey at yahoo.com Mon Oct 25 12:14:01 2010
From: sohaelshafey at yahoo.com (Soha Said)
Date: Mon, 25 Oct 2010 12:14:01 -0700 (PDT)
Subject: [protege-discussion] Rules Guide
Message-ID: <838598.10936.qm@web39608.mail.mud.yahoo.com>
Hello,
I want a guide to how write rules in rule view in menu view>ontology views>
rules.
I want some guide provides me with syntax and builtin keywords.
Thanks
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From tredmond at stanford.edu Mon Oct 25 16:20:18 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Mon, 25 Oct 2010 16:20:18 -0700
Subject: [protege-discussion] rdf visualization in protege?
In-Reply-To:
References:
Message-ID: <4CC610B2.9020909@stanford.edu>
On 10/21/2010 07:26 AM, Veronica Joh wrote:
> Hi
> I'm pretty new to protege, and I am trying to view rdf xml in Protege.
> Is it possible to load my rdf/xml in Protege and view the data inside it?
> I tried to load rdf/xml in Protege but I keep getting error saying the
> file is not well-formed.
What is the error. It is possible that Protege can load this file but
you need to do it in a different way.
> If this is not possible, can you please recommend any other tools that
> allows you to view data in RDF file, besides loading it to sesame?
First there are two Protege's that you can try. Usually one of them
will load an rdf file. But some RDF files are difficult to parse as OWL
and they will give parser errors.
I suspect that if Protege can't read the rdf file, there are some rdf
editors that you could choose. I know of TopBraid but there are
probably several. We are planning on building a Protege editor for this
purpose also.
-Timothy
> Thank you!
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From jonathan.carter at e-asolutions.com Tue Oct 26 04:45:22 2010
From: jonathan.carter at e-asolutions.com (Jonathan Carter)
Date: Tue, 26 Oct 2010 12:45:22 +0100
Subject: [protege-discussion] Programmatically override the maximum
cardinality for a slot, varying it by Cls
In-Reply-To:
References:
Message-ID: <6F2A3733-0613-4800-A703-6B474EF54DF4@e-asolutions.com>
Hi Ron,
I've been doing something similar recently with the Java API to programmatically apply updates to the Class and Slot hierarchy.
I believe that all you need to do is use the method:
setTemplateSlotMaximumCardinality(Slot slot, int max)
On the Cls class.
e.g.
articleCls = kb.getCls("Article");
keywordSlot = kb.getSlot("keyword");
articleCls.setTemplateSlotMaximumCardinality(keywordSlot, 5);
This is equivalent to editing the slot at the class rather than the top-level in the Protege GUI - which I believe is what you're looking for.
Hope this helps
Regards
Jonathan
_______________________________________
Jonathan Carter
Enterprise Architecture Solutions Ltd
_______________________________________
Proud sponsors of The Essential Project
The free open-source Enterprise Architecture Management Platform
www.enterprise-architecture.org
_______________________________________
Enterprise Architecture Solutions Ltd, Registered in England and Wales: 04097721.
Registered Office: 76 High Street, Newport Pagnell, Milton Keynes, MK16 8AQ.
On 25 Oct 2010, at 03:28, Ron Schultz wrote:
> I have a circumstance where different Clses contain the slot 'keyword.' The keyword slot is of valueType 'String,' with a default maximum cardinality set to 1.
>
> I have a requirement to vary this cardinality class by class. I am just not sure how to do this programmatically.
>
> Let's say I have a class 'Article' where I want to set the maximum number of keywords to 5.
>
> Do I:
> Get the slot 'keywords' from the cls 'Article', and then set the values of keyword's slot named :SLOT-MAXIMUM-CARDINALITY to a Collection containing 5?
> Or do I perform some operations using the facets of the slot 'keyword.'
> Or ...?
> I've spent all weekend trying to figure this out and I know I must be missing something obvious.
>
> Thanks.
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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From jonathan.carter at e-asolutions.com Tue Oct 26 04:47:28 2010
From: jonathan.carter at e-asolutions.com (Jonathan Carter)
Date: Tue, 26 Oct 2010 12:47:28 +0100
Subject: [protege-discussion] Programmatically override the maximum
cardinality for a slot, varying it by Cls
In-Reply-To: <6F2A3733-0613-4800-A703-6B474EF54DF4@e-asolutions.com>
References:
<6F2A3733-0613-4800-A703-6B474EF54DF4@e-asolutions.com>
Message-ID:
Apologies, I should have said that 'kb' represents a reference to the KnowledgeBase of your Project - I've been using the ScriptConsole to test stuff and this variable is defined by default in there!
Jonathan
_______________________________________
Jonathan Carter
Enterprise Architecture Solutions Ltd
_______________________________________
Proud sponsors of The Essential Project
The free open-source Enterprise Architecture Management Platform
www.enterprise-architecture.org
_______________________________________
Enterprise Architecture Solutions Ltd, Registered in England and Wales: 04097721.
Registered Office: 76 High Street, Newport Pagnell, Milton Keynes, MK16 8AQ.
On 26 Oct 2010, at 12:45, Jonathan Carter wrote:
> Hi Ron,
>
> I've been doing something similar recently with the Java API to programmatically apply updates to the Class and Slot hierarchy.
>
> I believe that all you need to do is use the method:
>
> setTemplateSlotMaximumCardinality(Slot slot, int max)
>
> On the Cls class.
>
> e.g.
>
> articleCls = kb.getCls("Article");
> keywordSlot = kb.getSlot("keyword");
> articleCls.setTemplateSlotMaximumCardinality(keywordSlot, 5);
>
> This is equivalent to editing the slot at the class rather than the top-level in the Protege GUI - which I believe is what you're looking for.
> Hope this helps
> Regards
>
> Jonathan
> _______________________________________
>
> Jonathan Carter
> Enterprise Architecture Solutions Ltd
> _______________________________________
>
> Proud sponsors of The Essential Project
> The free open-source Enterprise Architecture Management Platform
> www.enterprise-architecture.org
> _______________________________________
>
> Enterprise Architecture Solutions Ltd, Registered in England and Wales: 04097721.
> Registered Office: 76 High Street, Newport Pagnell, Milton Keynes, MK16 8AQ.
>
> On 25 Oct 2010, at 03:28, Ron Schultz wrote:
>
>> I have a circumstance where different Clses contain the slot 'keyword.' The keyword slot is of valueType 'String,' with a default maximum cardinality set to 1.
>>
>> I have a requirement to vary this cardinality class by class. I am just not sure how to do this programmatically.
>>
>> Let's say I have a class 'Article' where I want to set the maximum number of keywords to 5.
>>
>> Do I:
>> Get the slot 'keywords' from the cls 'Article', and then set the values of keyword's slot named :SLOT-MAXIMUM-CARDINALITY to a Collection containing 5?
>> Or do I perform some operations using the facets of the slot 'keyword.'
>> Or ...?
>> I've spent all weekend trying to figure this out and I know I must be missing something obvious.
>>
>> Thanks.
>> _______________________________________________
>> protege-discussion mailing list
>> protege-discussion at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
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From rcaschultz at gmail.com Tue Oct 26 05:17:43 2010
From: rcaschultz at gmail.com (Ron Schultz)
Date: Tue, 26 Oct 2010 07:17:43 -0500
Subject: [protege-discussion] Programmatically override the maximum
cardinality for a slot, varying it by Cls
In-Reply-To: <6F2A3733-0613-4800-A703-6B474EF54DF4@e-asolutions.com>
References:
<6F2A3733-0613-4800-A703-6B474EF54DF4@e-asolutions.com>
Message-ID:
Thanks Jonathan,
I researched the code within the *setTemplateSlotMaximumCardinality and
found what I needed. I was looking for a generic means of updating any
system facet - including the cardinality.*
**
Ron
On Tue, Oct 26, 2010 at 6:45 AM, Jonathan Carter <
jonathan.carter at e-asolutions.com> wrote:
> Hi Ron,
>
> I've been doing something similar recently with the Java API to
> programmatically apply updates to the Class and Slot hierarchy.
>
> I believe that all you need to do is use the method:
>
> *setTemplateSlotMaximumCardinality*(Slot slot,
> int max)
>
> On the Cls class.
>
> e.g.
>
> articleCls = kb.getCls("Article");
> keywordSlot = kb.getSlot("keyword");
> articleCls.setTemplateSlotMaximumCardinality(keywordSlot, 5);
>
> This is equivalent to editing the slot at the class rather than the
> top-level in the Protege GUI - which I believe is what you're looking for.
> Hope this helps
> Regards
>
> Jonathan
> _______________________________________
>
> Jonathan Carter
> Enterprise Architecture Solutions Ltd
> _______________________________________
>
> Proud sponsors of The Essential Project
> The free open-source Enterprise Architecture Management Platform
> www.enterprise-architecture.org
> _______________________________________
>
> Enterprise Architecture Solutions Ltd, Registered in England and Wales:
> 04097721.
> Registered Office: 76 High Street, Newport Pagnell, Milton Keynes, MK16
> 8AQ.
>
> On 25 Oct 2010, at 03:28, Ron Schultz wrote:
>
> I have a circumstance where different Clses contain the slot 'keyword.'
> The keyword slot is of valueType 'String,' with a default maximum
> cardinality set to 1.
>
> I have a requirement to vary this cardinality class by class. I am just not
> sure how to do this programmatically.
>
> Let's say I have a class 'Article' where I want to set the maximum number
> of keywords to 5.
>
> Do I:
>
> - Get the slot 'keywords' from the cls 'Article', and then set the
> values of keyword's slot named :SLOT-MAXIMUM-CARDINALITY to a Collection
> containing 5?
> - Or do I perform some operations using the facets of the slot
> 'keyword.'
> - Or ...?
>
> I've spent all weekend trying to figure this out and I know I must be
> missing something obvious.
>
> Thanks.
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
--
Ron
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From vjoh at inform.com Tue Oct 26 06:50:23 2010
From: vjoh at inform.com (Veronica Joh)
Date: Tue, 26 Oct 2010 09:50:23 -0400
Subject: [protege-discussion] rdf visualization in protege?
In-Reply-To: <4CC610B2.9020909@stanford.edu>
References:
<4CC610B2.9020909@stanford.edu>
Message-ID:
Thank you for your reply.
This is the error message I get when I try to open RDF/XML file on prot?g?.
1. Exception class edu.stanford.smi.protege.storage.clips.ParseException.
Message: Encountered " "
"(" ...
";+" ...
";+" ...
Can you please tell me how to load the file in prot?g??
Thank you!
Veronica
_____
From: protege-discussion-bounces at lists.stanford.edu
[mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Timothy
Redmond
Sent: Monday, October 25, 2010 7:20 PM
To: protege-discussion at lists.stanford.edu
Subject: Re: [protege-discussion] rdf visualization in protege?
On 10/21/2010 07:26 AM, Veronica Joh wrote:
Hi
I'm pretty new to protege, and I am trying to view rdf xml in Protege.
Is it possible to load my rdf/xml in Protege and view the data inside it?
I tried to load rdf/xml in Protege but I keep getting error saying the file
is not well-formed.
What is the error. It is possible that Protege can load this file but you
need to do it in a different way.
If this is not possible, can you please recommend any other tools that
allows you to view data in RDF file, besides loading it to sesame?
First there are two Protege's that you can try. Usually one of them will
load an rdf file. But some RDF files are difficult to parse as OWL and they
will give parser errors.
I suspect that if Protege can't read the rdf file, there are some rdf
editors that you could choose. I know of TopBraid but there are probably
several. We are planning on building a Protege editor for this purpose
also.
-Timothy
Thank you!
_______________________________________________
protege-discussion mailing list
protege-discussion at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
Instructions for unsubscribing:
http://protege.stanford.edu/doc/faq.html#01a.03
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From tredmond at stanford.edu Tue Oct 26 09:35:26 2010
From: tredmond at stanford.edu (Timothy Redmond)
Date: Tue, 26 Oct 2010 09:35:26 -0700
Subject: [protege-discussion] rdf visualization in protege?
In-Reply-To:
References: <4CC610B2.9020909@stanford.edu>
Message-ID: <4CC7034E.8090104@stanford.edu>
On 10/26/2010 06:50 AM, Veronica Joh wrote:
>
> Thank you for your reply.
>
> This is the error message I get when I try to open RDF/XML file on
> prot?g?.
>
> 1. Exception class edu.stanford.smi.protege.storage.clips.ParseException.
>
> Message: Encountered " "
> Was expecting one of:
>
>
>
> "(" ...
>
> ";+" ...
>
> ";+" ...
>
> Can you please tell me how to load the file in prot?g??
>
This is what I was wondering. This error has nothing to do with whether
Protege can parse rdf and has to do with Protege not realizing that this
was an rdf file.
I will give you an alternative way of loading the file that should work
better. In the opening screen click on New Project. Select the
checkbox at the top ("Create from Existing Sources") select "OWL/RDF
Files" and click "Next". Then you should be able to use the box with
the plus sign to select your rdf file. If the extension is rdf you may
need to tell the file browser to look for "Files of Type:" "All Files"
rather than "*.owl files".
-Timothy
> Thank you!
>
> Veronica
>
> ------------------------------------------------------------------------
>
> *From:* protege-discussion-bounces at lists.stanford.edu
> [mailto:protege-discussion-bounces at lists.stanford.edu] *On Behalf Of
> *Timothy Redmond
> *Sent:* Monday, October 25, 2010 7:20 PM
> *To:* protege-discussion at lists.stanford.edu
> *Subject:* Re: [protege-discussion] rdf visualization in protege?
>
> On 10/21/2010 07:26 AM, Veronica Joh wrote:
>
> Hi
>
> I'm pretty new to protege, and I am trying to view rdf xml in Protege.
>
> Is it possible to load my rdf/xml in Protege and view the data inside it?
>
> I tried to load rdf/xml in Protege but I keep getting error saying the
> file is not well-formed.
>
>
> What is the error. It is possible that Protege can load this file but
> you need to do it in a different way.
>
>
> If this is not possible, can you please recommend any other tools that
> allows you to view data in RDF file, besides loading it to sesame?
>
>
> First there are two Protege's that you can try. Usually one of them
> will load an rdf file. But some RDF files are difficult to parse as
> OWL and they will give parser errors.
>
> I suspect that if Protege can't read the rdf file, there are some rdf
> editors that you could choose. I know of TopBraid but there are
> probably several. We are planning on building a Protege editor for
> this purpose also.
>
> -Timothy
>
>
>
> Thank you!
>
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:http://protege.stanford.edu/doc/faq.html#01a.03
>
>
>
> _______________________________________________
> protege-discussion mailing list
> protege-discussion at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
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From vjoh at inform.com Tue Oct 26 11:36:55 2010
From: vjoh at inform.com (Veronica Joh)
Date: Tue, 26 Oct 2010 14:36:55 -0400
Subject: [protege-discussion] rdf visualization in protege?
In-Reply-To: <4CC7034E.8090104@stanford.edu>
References: <4CC610B2.9020909@stanford.edu>
<4CC7034E.8090104@stanford.edu>
Message-ID:
Thank you Timothy, I was able to open the RDF/XML file on prot?g?!
But what I really wanted was to be able to view actual values.
For example, I can see the Properties such as ?hasTopic? but is it possible
to view the actual topic value?
Or is this not possible in prot?g??
Thanks again,
Veronica
_____
From: protege-discussion-bounces at lists.stanford.edu
[mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Timothy
Redmond
Sent: Tuesday, October 26, 2010 12:35 PM
To: protege-discussion at lists.stanford.edu
Subject: Re: [protege-discussion] rdf visualization in protege?
On 10/26/2010 06:50 AM, Veronica Joh wrote:
Thank you for your reply.
This is the error message I get when I try to open RDF/XML file on prot?g?.
1. Exception class edu.stanford.smi.protege.storage.clips.ParseException.
Message: Encountered " "
"(" ...
";+" ...
";+" ...
Can you please tell me how to load the file in prot?g??
This is what I was wondering. This error has nothing to do with whether
Protege can parse rdf and has to do with Protege not realizing that this was
an rdf file.
I will give you an alternative way of loading the file that should work
better. In the opening screen click on New Project. Select the checkbox
at the top ("Create from Existing Sources") select "OWL/RDF Files" and click
"Next". Then you should be able to use the box with the plus sign to select
your rdf file. If the extension is rdf you may need to tell the file
browser to look for "Files of Type:" "All Files" rather than "*.owl files".
-Timothy
Thank you!
Veronica
_____
From: protege-discussion-bounces at lists.stanford.edu
[mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of Timothy
Redmond
Sent: Monday, October 25, 2010 7:20 PM
To: protege-discussion at lists.stanford.edu
Subject: Re: [protege-discussion] rdf visualization in protege?
On 10/21/2010 07:26 AM, Veronica Joh wrote:
Hi
I'm pretty new to protege, and I am trying to view rdf xml in Protege.
Is it possible to load my rdf/xml in Protege and view the data inside it?
I tried to load rdf/xml in Protege but I keep getting error saying the file
is not well-formed.
What is the error. It is possible that Protege can load this file but you
need to do it in a different way.
If this is not possible, can you please recommend any other tools that
allows you to view data in RDF file, besides loading it to sesame?
First there are two Protege's that you can try. Usually one of them will
load an rdf file. But some RDF files are difficult to parse as OWL and they
will give parser errors.
I suspect that if Protege can't read the rdf file, there are some rdf
editors that you could choose. I know of TopBraid but there are probably
several. We are planning on building a Protege editor for this purpose
also.
-Timothy
Thank you!
_______________________________________________
protege-discussion mailing list
protege-discussion at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
Instructions for unsubscribing:
http://protege.stanford.edu/doc/faq.html#01a.03
_______________________________________________
protege-discussion mailing list
protege-discussion at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
Instructions for unsubscribing:
http://protege.stanford.edu/doc/faq.html#01a.03
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From plwhetzel at gmail.com Fri Oct 29 14:50:09 2010
From: plwhetzel at gmail.com (Trish Whetzel)
Date: Fri, 29 Oct 2010 14:50:09 -0700
Subject: [protege-discussion] NCBO Webinar - Cecil Lynch,
Nov. 3 at 10:00am PT
In-Reply-To:
References:
Message-ID:
The next NCBO Webinar will be presented by Dr. Cecil Lynch from the
University of California School of Medicine at Davis on "Architecting an OWL
based Enterprise Conformance and Compliance Registry at the National Cancer
Institute" at 10:00am PDT, Wednesday, November 3. Below is information on
how to join the online meeting via WebEx and accompanying teleconference.
Please note there will not be a VOIP option and attendees must call into the
teleconference. For the full schedule of the NCBO Webinar presentations
see: http://www.bioontology.org/webinar-series.
ABSTRACT:
The National Cancer Institute (NCI) has long been a supporter of the
ontology community and a user of Prot?g? to maintain the NCI thesaurus. In
the next generation of the semantic infrastructure, the National Cancer
Institute is widening its use of semantic Web standards and tools and is
contributing back to the community with new tools and services.
In this talk we will go over the history of the use of ontologies at the NCI
in the management of it's vocabulary resources and discuss the new
terminology services and semantic infrastructure to support the NCI Center
for Biomedical Informatics and Information Technology. As part of the
Semantic Infrastructure Version 2 roadmap, the enterprise conformance and
compliance framework will be an owl-based metadata registry with the ability
to classify and test conformance of new metadata artifacts using description
logic and to link all artifacts within the metadata registry in context.
The NCI is evaluating tools for value set construction in owl formats, and
is investing in the development of a set of tools for the conversion of HL7
artifacts automatically to owl ontologies, thereby allowing the automated
expression of the next versions of the Biomedical Research Integrated Domain
Group (BRIDG) Model. The BRIDG model is a collaborative effort engaging
stakeholders from the Clinical Data Interchange Standards Consortium
(CDISC), the HL7 Regulated Clinical Research Information Management
Technical Committee (RCRIM TC), the National Cancer Institute (NCI) and its
Cancer Biomedical Informatics Grid (caBIG?), and the US Food and Drug
Administration (FDA). The BRIDG model is an instance of a Domain Analysis
Model (DAM). The goal of the BRIDG Model is to produce a shared view of the
dynamic and static semantics for the domain of protocol-driven research and
its associated regulatory artifacts. A joint domain analysis model for
clinical trials developed by the NCI, FDA, CDISC, and HL7.
We will also discuss some of the unexpected benefits of structuring the
BRIDG model in owl which will lead to improvements in open-source
reasoner's.
BIO:
Dr. Lynch is an assistant professor in pathology informatics at the
University of California at Davis. He completed his M.D. degree and a
residency in obstetrics and gynecology with an oncology emphasis at the
University of California at Los Angeles. He subsequently was in private
practice for more than 10 years in the Sacramento area before earning a
Master of science degree in medical informatics at the University California
at Davis in 2003. Dr. Lynch joined the faculty at UC Davis Medical School in
Medical Informatics and has served in several roles including past chair of
the graduate group in informatics. His area of interest has been in
decision-support and leveraging ontology in that realm.
He teaches courses on knowledge engineering and services-based enterprise
architecture to the graduate students at UC Davis. He currently has the role
as the Chief Semantic Architect at the National Cancer Institute where he is
participating in the design of the next generation semantic infrastructure.
Dr. Lynch is also the principal of a software engineering company called
OntoReason that specializes in knowledge engineering and enterprise
architecture for the federal health architecture and large integrated
hospital systems. In this role his team has built the ontology based
National surveillance System for Tuberculosis at the CDC and is currently
extending this ontology driven surveillance paradigm to H1N1.
Current Activities:
2010 - Present Chief Semantic Architect, National Cancer Institute
2010 - Present National Cancer Institute BRIDG Board of Directors
2008 - Present HHS appointed National Science Advisor to the National Center
for Public Health Informatics
2008 - Present HITSP Population Health Standards Committee CDC
representative for Decision Support and Case definition modeling
2008 - Present HHS Appointed National Science Advisor, National
Biosurveillance Advisory Sub-committee
2008 - Present Member, HL7 Architectural Review Board
2007 - Present Executive Committee Chair, Biosurveillance, Homeland
Security/HHS Joint Task Force for Critical Clinical and Public Health
Infrastructure Protection -
2006 - Present Member and Consulting Expert, European Union Centers for
Disease Control Knowledge Management Workgroup advising on ontology based
Semantic Infrastructure
WEBEX DETAILS:
Topic: NCBO Webinar Series
Date: Wednesday, November 3, 2010
Time: 10:00 am, Pacific Daylight Time (San Francisco, GMT-07:00)
Meeting Number: 926 719 478
Meeting Password: ncbomeeting
-------------------------------------------------------
To join the online meeting (Now from the Apple iPhone (R) and other
smartphones!)
-------------------------------------------------------
1. Go to
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NZDUwYTM4MmI3&RT=MiM0
2. If requested, enter your name and email address.
3. If a password is required, enter the meeting password: ncbomeeting
4. Click "Join".
5. Follow the instructions that appear on your screen.
To view in other time zones or languages, please click the link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&PW=NZDUwYTM4MmI3&ORT=MiM0
-------------------------------------------------------
To join the audio conference only
-------------------------------------------------------
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:
https://stanford.webex.com/stanford/globalcallin.php?serviceType=MC&ED=107799137&tollFree=0
Access code:926 719 478
-------------------------------------------------------
For assistance
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/mc
2. On the left navigation bar, click "Support".
You can contact me at:
whetzel at stanford.edu
To update this meeting to your calendar program (for example Microsoft
Outlook), click this link:
https://stanford.webex.com/stanford/j.php?ED=107799137&UID=0&ICS=UMI&LD=1&RD=2&ST=1&SHA2=sscJxPSrxubkyAnBruXELuZe4XBKeHnhQa70aJiFfUI=&RT=MiM0
WebEx will automatically setup Meeting Manager for Windows the first time
you join a meeting. To save time, you can setup prior to the meeting by
clicking this link:
https://stanford.webex.com/stanford/meetingcenter/mcsetup.php
http://www.webex.com
CCP:+16504293300x926719478#
IMPORTANT NOTICE: This WebEx service includes a feature that allows audio
and any documents and other materials exchanged or viewed during the session
to be recorded. By joining this session, you automatically consent to such
recordings. If you do not consent to the recording, discuss your concerns
with the meeting host prior to the start of the recording or do not join the
session. Please note that any such recordings may be subject to discovery in
the event of litigation.
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